sp|Q9FM80|MTEF9_ARATH ----> Transcription termination factor MTERF9, chloroplastic

Intron 1 GTAAAACTTG ... ACTGCTCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	52	24	7.7	26
A2	40	27	0.7	18
A3	39.76	50	5.3	33
A4	50.7	35	1	36
A5	51.35	18	2.3	19
A6	36.95	71.7	1.7	42
A7	42.75	79	4	59
A8	47.96	51	2	47
A9	38.4	77	7	48
A10	45.52	85	11.7	71

>TRINITY_DN109840_c1_g1_i7 from sample A2 / Example spliced isoform

CACTGGTAAAAATAAATCCAGGTTACGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCG
ACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGT
GGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGC
CGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAA
AGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAAC
ATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAA
TAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAG
GACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGA
GCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGGTGATTTTTCATTTCTCCAGCTGATTTATTTGAGGTTTTCAATGCGT
AAGGTATACTTCCATATTCCTAAGCATATATCAATTATTTCCCATATTCCTAAGCATATGAAATGTATGCTTTTGTTTCTCTGTACACCGAGGTTGACAATATTATTCATTCTAAGCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCA
TTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGG
TGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCC
CAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGAC
TTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATC
CTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTG

>TRINITY_DN109840_c1_g1_i5 from sample A2 / Example unspliced isoform:

CACTGGTAAAAATAAATCCAGGTTACGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGgtaaaacttgtttttatctaaatttttagtttctgaacggtggtgaatc
gattttccgttaattaaaattcacagcactctgaaaaacttcttaaaccctgactctggttgcgggcgggaaaatctttattccgcctttgagattgttgaagctgtaaatttctaatttgctcggggattttgtcaaaataatgcccggaatcatctgtttctagaggttgatgtagttcggcactggaaaagaatgat
ttagatatttgaagtttgaaagcaatgttatttacattatctttttagaataatggaagtttgattacataattatgtttgaattaagttcaaaattcagctccattagatattaaagccgtggataaggttttttctagtcacaaatggacggctgataatttgtctgcatgcactgctccagAGAGAGATAAATCTTT
ATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATG
TTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCG
TTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGA
AGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAG
AAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGG
CTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTT
TGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAA
TCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGGTGATTTTTCATTT
CTCCAGCTGATTTATTTGAGGTTTTCAATGCGTAAGGTATACTTCCATATTCCTAAGCATATATCAATTATTTCCCATATTCCTAAGCATATGAAATGTATGCTTTTGTTTCTCTGTACACCGAGGTTGACAATATTATTCATTCTAAGCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTAT
TTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCA
AGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAA
ACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTT
GCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTG
TCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTG

Intron 2 GTGATTTTTC ... TTCTAAGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	37.36	21	18.2	7
A2	28.62	22	6.7	11
A3	15.42	26	6.5	3
A4	43.98	5	2.9	5
A5	34.65	10	4.7	6
A6	35.42	8	4.8	4
A7	27.82	43	25.5	8
A8	40.8	45	44.3	18
A9	22.65	41	14.1	10
A10	30.1	50	15.1	28

>TRINITY_DN114823_c0_g1_i12 from sample A1 / Example spliced isoform

CGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCGTTAATTAAAATTCACA
GCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGATTTTGTCAAAATAATGCCCGGAATCATCTGTTTCTAGAGGTTGATGTAGTTCGGCACTGGAAAAGAATGATTTAGATATTTGAAGTTTGAAAGCAA
TGTTATTTACATTATCTTTTTAGAATAATGGAAGTTTGATTACATAATTATGTTTGAATTAAGTTCAAAATTCAGCTCCATTAGATATTAAAGCCGTGGATAAGGTTTTTTCTAGTCACAAATGGACGGCTGATAATTTGTCTGCATGCACTGCTCCAGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAA
GAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGG
ACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCAT
GACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGT
TCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAAT
CTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGA
ATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTC
CCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGG
AGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAA
TATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATAC
AACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCG
TTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAG
TGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGC
TGTCTTTTGTCAGCGTTATATTTTCAAATCAGG

>TRINITY_DN114823_c0_g1_i10 from sample A1 / Example unspliced isoform:

CGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCGTTAATTAAAATTCACA
GCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGATTTTGTCAAAATAATGCCCGGAATCATCTGTTTCTAGAGGTTGATGTAGTTCGGCACTGGAAAAGAATGATTTAGATATTTGAAGTTTGAAAGCAA
TGTTATTTACATTATCTTTTTAGAATAATGGAAGTTTGATTACATAATTATGTTTGAATTAAGTTCAAAATTCAGCTCCATTAGATATTAAAGCCGTGGATAAGGTTTTTTCTAGTCACAAATGGACGGCTGATAATTTGTCTGCATGCACTGCTCCAGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAA
GAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGG
ACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCAT
GACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGT
TCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAAT
CTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGA
ATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTC
CCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGG
AGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGgtgatttttcatttctccagctgatttatttgaggtttt
caatgcgtaaggtatacttccatattcctaagcatatatcaattatttcccatattcctaagcatatgaaatgtatgcttttgtttctctgtacaccgaggttgacaatattattcattctaagcagATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAG
TTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACAATTG
TTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAAT
AAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGA
ACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGG

Intron 3 GTAAGTTCAT ... TGTGTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	40	18	9	12
A2	39.39	20	1	13
A3	36.36	7	2	4
A4	42.31	15	1	11
A5	37.5	5	0	3
A6	44.56	107	4	86
A7	40.76	109	9	75
A8	40.7	169	30	116
A9	37.99	173	24	106
A10	41.07	66	6	46

>TRINITY_DN37657_c0_g1_i27 from sample A6 / Example spliced isoform

AATAAATCCAGGTTACGACGAAATGACATCTGGCGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGG
AATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACC
CCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAA
GACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAG
GAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTT
CCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGA
ACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCC
ATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGA
AAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGGTGATTTTTCATTTCTCCAGCTGATTTATTTGAGGTTTTCAATGCGTAAGTGGAGAAGAATCTGCGCCC
CAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTG
ATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGA
AGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTG
TTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCA
AAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAAGTCGGCATCGGCA

>TRINITY_DN37657_c0_g1_i10 from sample A6 / Example unspliced isoform:

AATAAATCCAGGTTACGACGAAATGACATCTGGCGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGG
AATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACC
CCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAA
GACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAG
GAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTT
CCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGA
ACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCC
ATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGA
AAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAAT
GGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACA
ATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCT
GAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGgtaagttcattgcaagtcttactaaacaatttctatatttctgtgacatcaaacagtggaaaatct
tgacattatatcttaaatttgtgacaccaaaaggtattttattctacatgctgactggtgtttggttctgtgtttcagGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAA
AGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTT
TAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAAGTCGGCATCGGCA

Intron 4 GTGATTTTTC ... AATGCGTAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	26.15	24	11	6
A2	23.08	25	5	10
A3	20	28	7	7
A4	33.33	5	2	3
A5	39.13	7	2	7
A6	33.33	8	4	4
A7	27.13	47	19	16
A8	31.82	45	21	21
A9	25.19	49	14	19
A10	18.03	50	10	12

>TRINITY_DN37657_c0_g1_i13 from sample A6 / Example spliced isoform

AATAAATCCAGGTTACGACGAAATGACATCTGGCGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGG
AATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACC
CCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAA
GACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAG
GAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTT
CCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGA
ACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCC
ATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGA
AAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTAT
CAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAG
TTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGA
ATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCA
GATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCA
AAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAAGTCGGCATCGGCA

>TRINITY_DN37657_c0_g1_i27 from sample A6 / Example unspliced isoform:

AATAAATCCAGGTTACGACGAAATGACATCTGGCGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGG
AATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACC
CCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAA
GACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAG
GAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTT
CCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGA
ACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCC
ATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGA
AAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGgtgatttttcatttctccagctgatttatttgaggttttcaatgcgtaagTGGAGAAGAATCTGCGCCC
CAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTG
ATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGA
AGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTG
TTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCA
AAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAAGTCGGCATCGGCA

Intron 5 GTTGATGTAG ... ACTGCTCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	48.15	28	8	26
A2	46.15	21	5	18
A3	46.48	38	12	33
A4	50.7	35	5	36
A5	47.5	21	0	19
A6	45.16	51	2	42
A7	44.7	73	3	59
A8	45.19	57	7	47
A9	47.52	53	2	48
A10	50.71	69	5	71

>TRINITY_DN109840_c1_g1_i8 from sample A2 / Example spliced isoform

CACTGGTAAAAATAAATCCAGGTTACGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATC
GATTTTCCGTTAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGATTTTGTCAAAATAATGCCCGGAATCATCTGTTTCTAGAGAGAGAGATAAATCTTTATATGGCGACACGTTA
AAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCC
TACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAAT
TGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAA
AGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAAT
CTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCAC
TTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGT
GCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTC
TTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGGTGATTTTTCATTTCTCCAGCTGATTTATT
TGAGGTTTTCAATGCGTAAGGTATACTTCCATATTCCTAAGCATATATCAATTATTTCCCATATTCCTAAGCATATGAAATGTATGCTTTTGTTTCTCTGTACACCGAGGTTGACAATATTATTCATTCTAAGCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCG
AAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTT
CGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGC
ATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTT
CAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTC
AAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTG

>TRINITY_DN109840_c1_g1_i5 from sample A2 / Example unspliced isoform:

CACTGGTAAAAATAAATCCAGGTTACGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATC
GATTTTCCGTTAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGATTTTGTCAAAATAATGCCCGGAATCATCTGTTTCTAGAGgttgatgtagttcggcactggaaaagaatgat
ttagatatttgaagtttgaaagcaatgttatttacattatctttttagaataatggaagtttgattacataattatgtttgaattaagttcaaaattcagctccattagatattaaagccgtggataaggttttttctagtcacaaatggacggctgataatttgtctgcatgcactgctccagAGAGAGATAAATCTTT
ATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATG
TTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCG
TTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGA
AGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAG
AAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGG
CTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTT
TGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAA
TCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGGTGATTTTTCATTT
CTCCAGCTGATTTATTTGAGGTTTTCAATGCGTAAGGTATACTTCCATATTCCTAAGCATATATCAATTATTTCCCATATTCCTAAGCATATGAAATGTATGCTTTTGTTTCTCTGTACACCGAGGTTGACAATATTATTCATTCTAAGCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTAT
TTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCA
AGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAA
ACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTT
GCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTG
TCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTG

Intron 6 GTTACAAACA ... AGATTACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	63.64	14	26	23
A2	52.69	22	25	24
A3	57.89	16	20	24
A4	49.02	13	13	12
A5	57.14	6	14	2
A6	49.37	20	12	27
A7	61.36	68	112	104
A8	59.12	56	69	93
A9	64.81	41	71	80
A10	59.31	47	63	74

>TRINITY_DN41783_c0_g1_i11 from sample A10 / Example spliced isoform

CGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCG
CTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTAT
ACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGAC
AGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGT
TAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCA
CGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCC
CAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAG
CTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATC
CACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCA
GCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAAC
TGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGA
AGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTG
ATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAAGTCGGCACCGGC

>TRINITY_DN41783_c0_g1_i1 from sample A10 / Example unspliced isoform:

CGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGA
ACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTC
TTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTAC
GGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGG
TACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGA
GATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAA
GTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTT
CTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGG
TCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGGTGATTTTTCATTTCTCCAGCTGATTTATTTGAGGTTTTCAATGCGTAAGGTATACTTCCATATTCCTAAGCATA
TATCAATTATTTCCCATATTCCTAAGCATATGAAATGTATGCTTTTGTTTCTCTGTACACCGAGGTTGACAATATTATTCATTCTAAGCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCA
TATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGgttacaaacagacctttccctataaaagccttacttgttaatgatgactgtttctgtaagcggtgggctgatacaactcttcaagattaccagGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAG
CAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATA
TTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTT
CATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAA
CCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAAGTCGGCACCGGC

Intron 7 GTAAATTTCT ... GTTTCTAGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	54.9	23	10	28
A2	52.5	19	9	21
A3	56.72	29	18	38
A4	59.32	24	6	35
A5	53.85	18	13	21
A6	52.58	46	12	51
A7	58.4	52	19	73
A8	54.29	48	20	57
A9	54.08	45	12	53
A10	55.2	56	25	69

>TRINITY_DN37657_c0_g1_i17 from sample A6 / Example spliced isoform

AATAAATCCAGGTTACGACGAAATGACATCTGGCGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCAT
TAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTAC
GTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGT
ATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTAC
CTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTG
CACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAA
TTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATT
TCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTG
AAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTA
CAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATT
TCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCA
CAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTA
ATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAG
GAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGT
CCATAACCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAAGTCGGCATCGGCA

>TRINITY_DN37657_c0_g1_i25 from sample A6 / Example unspliced isoform:

AATAAATCCAGGTTACGACGAAATGACATCTGGCGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCAT
TAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTgtaaatttctaatttgctcggggattttgtcaaaataatgcccggaatcatctgtttctagagAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAG
AACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGA
CTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATG
ACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTT
CTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATC
TGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAA
TTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCC
CGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGA
GCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAAT
ATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACA
ACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGT
TGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGT
GATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCT
GTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAAGTCGGCATCGGCA

Intron 8 GTGATTTTTC ... TCTCTGTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	36.84	24	19	9
A2	29.58	25	7	14
A3	20	28	7	7
A4	41.18	5	3	4
A5	44	7	5	6
A6	36	8	5	4
A7	30.88	47	27	15
A8	44.1	45	46	25
A9	25.19	49	15	18
A10	30.56	50	16	28

>TRINITY_DN114823_c0_g1_i1 from sample A1 / Example spliced isoform

CGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGAC
CCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTT
TATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATT
GACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAG
GGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCT
CCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCA
GCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTA
TAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGC
ATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTAT
ATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTT
TCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAA
GTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAG
AAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGG

>TRINITY_DN114823_c0_g1_i13 from sample A1 / Example unspliced isoform:

CGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGAC
CCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTT
TATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATT
GACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAG
GGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCT
CCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCA
GCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTA
TAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGC
ATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGgtgatttttcatttctccagctgatttatttgaggttttcaatgcgtaaggtatacttccatattcctaagcatatatcaatta
tttcccatattcctaagcatatgaaatgtatgcttttgtttctctgtacaccgaggttgacaatattattcattctaagcagattttgtctctgtcagTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTA
AACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTT
GACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCAT
AACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTC
ATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGG

Intron 9 GTGCTTCTAC ... TGTGTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	61.54	15	36	12
A2	45.05	25	28	13
A3	58.82	14	36	4
A4	37.86	32	28	11
A5	60	4	9	3
A6	27.36	146	24	86
A7	39.18	111	68	75
A8	33.99	134	22	116
A9	30.39	189	59	106
A10	36.31	107	76	46

>TRINITY_DN38863_c0_g1_i1 from sample A8 / Example spliced isoform

GCGGAATGAATCTTCTGCGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCATTAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGA
TTTTGTCAAAATAATGCCCGGAATCATCTGTTTCTAGAGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGA
ATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTA
TACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTT
TCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATC
AGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGT

>TRINITY_DN38863_c0_g1_i2 from sample A8 / Example unspliced isoform:

AGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCT
TATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGT
GCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATgtgcttctacctggggaacacacttatgtggatgctgataatgccaagtctgcagaaacaaccttttcttccacgtcactgggtgcattctcaggacaatccttc
catgaacaagaactgaagcaaggaaaaacaaaagcaaatgttcttcaaaagactggaaagaggttggctaggaatggtacggtgagggttaattcattgggcctgcacccttcccctttgaggctacctcgaaatgagtgggagaagagagcctttgagatcatacggcagcagaaattaagaaatattgaactagaaag
gaagcgaagcgagcagaaaatattgcttgaatctcctaaatctgaaaacattgaccagattatagaaagttcccagagattaggctccacgaatgcaaacttgaattatgaggttacagctggaaacattgaggatgttgaatatcaattgatggcaaagcgattaggttttgaagcaaaatggaaacccttgattcagt
atttgagtagccttggcttaaatgagtgtcactttgcccgaatttataataggcacaaacctaccctaagaacaaaagtatcatcagcccaggaaagattggatttcttacaaagtgtgggtgtcaaaactgaggatttggtgaaaatcattctaaaacaacctcaaatcttagggtatacaattgagaataacataaaa
ccacatattgactttttgagaggcttgggggtgcctgattcccggttaggacaaataataacagcaaatccatctttcttttcttatagcttggagttgtctctgaagccaaaggtaagatttttaaccgaggaagttggcattaaaagaacagacttggggaaagttgtgattctaggccctgagatactgagacaacc
tgctgaagccttgaaatctcggttagaatttctttcaaaggagcttggagcatcaaagggaaatctagtgaaaatggtcacaaagcatccacagcttctccactacagcattaccgatggtatacagccacgaatcaattttttgaggagcattggcatgaatgaggctgacattgtgaaagttttaacaagattacccc
aggtgatttttcatttctccagctgatttatttgaggttttcaatgcgtaaggtatacttccatattcctaagcatatatcaattatttcccatattcctaagcatatgaaatgtatgcttttgtttctctgtacaccgaggttgacaatattattcattctaagcagattttgtctctgtcagtggagaagaatctgcg
ccccaaatatttgtatttagtcaaagaactcgaaaatggagttgagtcattatcagcacaccccttatatttcagcatatcgcttaaacaacgcatttggcctcgtcacagattcttgacttccctgaaaaaggttacaaacagacctttccctataaaagccttacttgttaatgatgactgtttctgtaagcggtggg
ctgatacaactcttcaagattaccaggcatttcgacaattgttactgggtgagttggcaggggaggtttcacagaagcagggcgttgacatgtgattaaatatggagcatacaaaatagcattacatttgcaggtgctgacatcaaactgtgtactgatggtagtctacagaaaccattgcgagatgaaccttctgagat
agaagcgttgttggaaacagaaagcctattgcattctgaataagcctcccagaatctcaaaattctaagtaatgatattgaatcataaccatggtgatacccttctgaaagtatccttacattcgcgaccgttttatccaaagttggaagttgtaacattgatgctaattggtaagttcattgcaagtcttactaaacaa
tttctatatttctgtgacatcaaacagtggaaaatcttgacattatatcttaaatttgtgacaccaaaaggtattttattctacatgctgactggtgtttggttctgtgtttcagGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGAT
ATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAA
CAGTGTATTCTCCGTCCATAACCCCAGT

Intron 10 GTGCTTCTAC ... TGTGTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	61.54	15	36	12
A2	45.05	25	28	13
A3	58.82	14	36	4
A4	37.86	32	28	11
A5	60	4	9	3
A6	27.36	146	24	86
A7	39.18	111	68	75
A8	33.99	134	22	116
A9	30.39	189	59	106
A10	36.31	107	76	46

>TRINITY_DN37657_c0_g1_i26 from sample A6 / Example spliced isoform

AATAAATCCAGGTTACGACGAAATGACATCTGGCGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGG
TGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAG
GATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTT
GAGGATGACGAAGACTACGGTACTATTGACAGTGATGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGG
ATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAA
GTCGGCATCGGCA

>TRINITY_DN37657_c0_g1_i10 from sample A6 / Example unspliced isoform:

AATAAATCCAGGTTACGACGAAATGACATCTGGCGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGG
AATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACC
CCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAA
GACTACGGTACTATTGACAGTGATgtgcttctacctggggaacacacttatgtggatgctgataatgccaagtctgcagaaacaaccttttcttccacgtcactgggtgcattctcaggacaatccttccatgaacaagaactgaagcaaggaaaaacaaaagcaaatgttcttcaaaagactggaaagaggttggctag
gaatggtacggtgagggttaattcattgggcctgcacccttcccctttgaggctacctcgaaatgagtgggagaagagagcctttgagatcatacggcagcagaaattaagaaatattgaactagaaaggaagcgaagcgagcagaaaatattgcttgaatctcctaaatctgaaaacattgaccagattatagaaagtt
cccagagattaggctccacgaatgcaaacttgaattatgaggttacagctggaaacattgaggatgttgaatatcaattgatggcaaagcgattaggttttgaagcaaaatggaaacccttgattcagtatttgagtagccttggcttaaatgagtgtcactttgcccgaatttataataggcacaaacctaccctaaga
acaaaagtatcatcagcccaggaaagattggatttcttacaaagtgtgggtgtcaaaactgaggatttggtgaaaatcattctaaaacaacctcaaatcttagggtatacaattgagaataacataaaaccacatattgactttttgagaggcttgggggtgcctgattcccggttaggacaaataataacagcaaatcc
atctttcttttcttatagcttggagttgtctctgaagccaaaggtaagatttttaaccgaggaagttggcattaaaagaacagacttggggaaagttgtgattctaggccctgagatactgagacaacctgctgaagccttgaaatctcggttagaatttctttcaaaggagcttggagcatcaaagggaaatctagtga
aaatggtcacaaagcatccacagcttctccactacagcattaccgatggtatacagccacgaatcaattttttgaggagcattggcatgaatgaggctgacattgtgaaagttttaacaagattaccccagattttgtctctgtcagtggagaagaatctgcgccccaaatatttgtatttagtcaaagaactcgaaaat
ggagttgagtcattatcagcacaccccttatatttcagcatatcgcttaaacaacgcatttggcctcgtcacagattcttgacttccctgaaaaaggttacaaacagacctttccctataaaagccttacttgttaatgatgactgtttctgtaagcggtgggctgatacaactcttcaagattaccaggcatttcgaca
attgttactgggtgagttggcaggggaggtttcacagaagcagggcgttgacatgtgattaaatatggagcatacaaaatagcattacatttgcaggtgctgacatcaaactgtgtactgatggtagtctacagaaaccattgcgagatgaaccttctgagatagaagcgttgttggaaacagaaagcctattgcattct
gaataagcctcccagaatctcaaaattctaagtaatgatattgaatcataaccatggtgatacccttctgaaagtatccttacattcgcgaccgttttatccaaagttggaagttgtaacattgatgctaattggtaagttcattgcaagtcttactaaacaatttctatatttctgtgacatcaaacagtggaaaatct
tgacattatatcttaaatttgtgacaccaaaaggtattttattctacatgctgactggtgtttggttctgtgtttcagGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAA
AGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTT
TAGTTTGCTGTTAAAATATTGATTTCTCGCAATGTTGAAAAAGTCGGCATCGGCA

Intron 11 GTGCTTCTAC ... TGTGTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	61.54	15	36	12
A2	45.05	25	28	13
A3	58.82	14	36	4
A4	37.86	32	28	11
A5	60	4	9	3
A6	27.36	146	24	86
A7	39.18	111	68	75
A8	33.99	134	22	116
A9	30.39	189	59	106
A10	36.31	107	76	46

>TRINITY_DN38863_c0_g1_i1 from sample A8 / Example spliced isoform

GCGGAATGAATCTTCTGCGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCATTAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGA
TTTTGTCAAAATAATGCCCGGAATCATCTGTTTCTAGAGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGA
ATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTA
TACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTT
TCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATC
AGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGT

>TRINITY_DN38863_c0_g1_i20 from sample A8 / Example unspliced isoform:

AGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCT
TATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGT
GCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATgtgcttctacctggggaacacacttatgtggatgctgataatgccaagtctgcagaaacaaccttttcttccacgtcactgggtgcattctcaggacaatccttc
catgaacaagaactgaagcaaggaaaaacaaaagcaaatgttcttcaaaagactggaaagaggttggctaggaatggtacggtgagggttaattcattgggcctgcacccttcccctttgaggctacctcgaaatgagtgggagaagagagcctttgagatcatacggcagcagaaattaagaaatattgaactagaaag
gaagcgaagcgagcagaaaatattgcttgaatctcctaaatctgaaaacattgaccagattatagaaagttcccagagattaggctccacgaatgcaaacttgaattatgaggtatagttgaaatttcgcaaattgctaaatgtgacagacttttcatcctccaattattttctatccatgtgggtcttatgcaattaca
tgttcaatgtttttccctgttggaaggttgaagactggtttgccttttttaatttcttttcaggttacagctggaaacattgaggatgttgaatatcaattgatggcaaagcgattaggttttgaagcaaaatggaaacccttgattcagtatttgagtagccttggcttaaatgagtgtcactttgcccgaatttataa
taggcacaaacctaccctaagaacaaaagtatcatcagcccaggaaagattggatttcttacaaagtgtgggtgtcaaaactgaggatttggtgaaaatcattctaaaacaacctcaaatcttagggtatacaattgagaataacataaaaccacatattgactttttgagaggcttgggggtgcctgattcccggttag
gacaaataataacagcaaatccatctttcttttcttatagcttggagttgtctctgaagccaaaggtaagatttttaaccgaggaagttggcattaaaagaacagacttggggaaagttgtgattctaggccctgagatactgagacaacctgctgaagccttgaaatctcggttagaatttctttcaaaggagcttgga
gcatcaaagggaaatctagtgaaaatggtcacaaagcatccacagcttctccactacagcattaccgatggtatacagccacgaatcaattttttgaggagcattggcatgaatgaggctgacattgtgaaagttttaacaagattaccccaggtgatttttcatttctccagctgatttatttgaggttttcaatgcgt
aaggtatacttccatattcctaagcatatatcaattatttcccatattcctaagcatatgaaatgtatgcttttgtttctctgtacaccgaggttgacaatattattcattctaagcagattttgtctctgtcagtggagaagaatctgcgccccaaatatttgtatttagtcaaagaactcgaaaatggagttgagtca
ttatcagcacaccccttatatttcagcatatcgcttaaacaacgcatttggcctcgtcacagattcttgacttccctgaaaaaggttacaaacagacctttccctataaaagccttacttgttaatgatgactgtttctgtaagcggtgggctgatacaactcttcaagattaccaggcatttcgacaattgttactggg
tgagttggcaggggaggtttcacagaagcagggcgttgacatgtgattaaatatggagcatacaaaatagcattacatttgcaggtgctgacatcaaactgtgtactgatggtagtctacagaaaccattgcgagatgaaccttctgagatagaagcgttgttggaaacagaaagcctattgcattctgaataagcctcc
cagaatctcaaaattctaagtaatgatattgaatcataaccatggtgatacccttctgaaagtatccttacattcgcgaccgttttatccaaagttggaagttgtaacattgatgctaattggtaagttcattgcaagtcttactaaacaatttctatatttctgtgacatcaaacagtggaaaatcttgacattatatc
ttaaatttgtgacaccaaaaggtattttattctacatgctgactggtgtttggttctgtgtttcagGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATA
TGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGT

Intron 12 GTATAGTTGA ... TTCTTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	24.62	49	18.8	16
A2	20.69	23	13.5	6
A3	27.08	35	11.9	13
A4	21.21	26	8.3	7
A5	15.38	11	3.6	2
A6	30	14	2.7	6
A7	34.18	52	23.6	27
A8	32.35	46	18.5	22
A9	25.3	62	26.3	21
A10	24.42	65	25.1	21

>TRINITY_DN119591_c0_g1_i1 from sample A3 / Example spliced isoform

CATTCTTCTAACAGTAACACTGGTAAAAATAAATCCAGGTTACGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGT
GAATCGATTTTCCGTTAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGATTTTGTCAAAATAATGCCCGGAATCATCTGTTTCTAGAGAGAGAGATAAATCTTTATATGGCGACA
CGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTAC
TTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGAT
GCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAA
ACAAAAGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCT
TGAATCTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGT
GTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTG
GGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGA
ATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGATTTTGTCTCTGTCAGTGGAGAAGA
ATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAG
CGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTT
CTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGT
TTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGAT
CAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAA

>TRINITY_DN119591_c0_g1_i4 from sample A3 / Example unspliced isoform:

AATGCAAACTTGAATTATGAGgtatagttgaaatttcgcaaattgctaaatgtgacagacttttcatcctccaattattttctatccatgtgggtcttatgcaattacatgttcaatgtttttccctgttggaaggttgaagactggtttgccttttttaatttcttttcagGTTACAGCTGGAAACATTGAGGATGTTG
AATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTG
GTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGG
CATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATT
TTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGT
CACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGA
GCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCT
GAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATAT
GGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAA

Intron 13 GTTGATGTAG ... ACTGCTCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	48.15	28	8	26
A2	46.15	21	5	18
A3	46.48	38	12	33
A4	50.7	35	5	36
A5	47.5	21	0	19
A6	45.16	51	2	42
A7	44.7	73	3	59
A8	45.19	57	7	47
A9	47.52	53	2	48
A10	50.71	69	5	71

>TRINITY_DN41783_c0_g1_i3 from sample A10 / Example spliced isoform

TTCTGCGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCGTTAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGATTTTGTCAAAAT
AATGCCCGGAATCATCTGTTTCTAGAGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCG
TATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAA
ATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATG

>TRINITY_DN41783_c0_g1_i5 from sample A10 / Example unspliced isoform:

TTCTGCGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCGTTAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGATTTTGTCAAAAT
AATGCCCGGAATCATCTGTTTCTAGAGgttgatgtagttcggcactggaaaagaatgatttagatatttgaagtttgaaagcaatgttatttacattatctttttagaataatggaagtttgattacataattatgtttgaattaagttcaaattcagctccattagatattaaagccgtggataaggttttttctagtc
acaaatggacggctgataatttgtctgcatgcactgctccagAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACA
CGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGT
GTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATG

Intron 14 GTGCTTCTAC ... TGTGTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	61.54	15	36	12
A2	45.05	25	28	13
A3	58.82	14	36	4
A4	37.86	32	28	11
A5	60	4	9	3
A6	27.36	146	24	86
A7	39.18	111	68	75
A8	33.99	134	22	116
A9	30.39	189	59	106
A10	36.31	107	76	46

>TRINITY_DN46179_c3_g1_i1 from sample A7 / Example spliced isoform

TACTTGGAGTTTTAAAGTTAATAGATTATCAATAACAATAATGAAATAAATAAATAAATGCCAAAAAGAAACTCCATTGTTATGTAAATACACGTAACAATGGAAATCGAACACGTGTTCAGTGAAAAACTTCCATCGATTAGCTGCGGCACAGCTCAGCCGACCAAATATTTCATTCTTCTAACAGTAACACTGGTAAA
AATAAATCCAGGTTACGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCGT
TAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGATTTTGTCAAAATAATGCCCGGAATCATCTGTTTCTAGAGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAG
AACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGA
CTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATG
ACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGT
AAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATTGATTT
CTCGCAATGTTGAAAAAGTCGGCATCGACAAAAAGTCGGCAAGGGTCCTGAATACAACTTCTCGGCAACATCG

>TRINITY_DN46179_c3_g1_i2 from sample A7 / Example unspliced isoform:

TACTTGGAGTTTTAAAGTTAATAGATTATCAATAACAATAATGAAATAAATAAATAAATGCCAAAAAGAAACTCCATTGTTATGTAAATACACGTAACAATGGAAATCGAACACGTGTTCAGTGAAAAACTTCCATCGATTAGCTGCGGCACAGCTCAGCCGACCAAATATTTCATTCTTCTAACAGTAACACTGGTAAA
AATAAATCCAGGTTACGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGGTAAAACTTGTTTTTATCTAAATTTTTAGTTTCTGAACGGTGGTGAATCGATTTTCCGT
TAATTAAAATTCACAGCACTCTGAAAAACTTCTTAAACCCTGACTCTGGTTGCGGGCGGGAAAATCTTTATTCCGCCTTTGAGATTGTTGAAGCTGTAAATTTCTAATTTGCTCGGGGATTTTGTCAAAATAATGCCCGGAATCATCTGTTTCTAGAGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAG
AACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGA
CTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATG
ACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATgtgcttctacctggggaacacacttatgtggatgctgataatgccaagtctgcagaaacaaccttttcttccacgtcactgggtgcattctcaggacaatccttccatgaacaagaactgaagcaaggaaaaacaaaagcaaatgtt
cttcaaaagactggaaagaggttggctaggaatggtacggtgagggttaattcattgggcctgcacccttcccctttgaggctacctcgaaatgagtgggagaagagagcctttgagatcatacggcagcagaaattaagaaatattgaactagaaaggaagcgaagcgagcagaaaatattgcttgaatctcctaaatc
tgaaaacattgaccagattatagaaagttcccagagattaggctccacgaatgcaaacttgaattatgaggtatagttgaaatttcgcaaattgctaaatgcgacagacttttcatcctccaattattttctatccatgtgggtcttatgcaattacatgttcaatgtttttccctgttggaaggttgaagactggtttg
ccttttttaatttcttttcaggttacagctggaaacattgaggatgttgaatatcaattgatggcaaagcgattaggttttgaagcaaaatggaaacccttgattcagtatttgagtagccttggcttaaatgagtgtcactttgcccgaatttataataggcacaaacctaccctaagaacaaaagtatcatcagccca
ggaaagattggatttcttacaaagtgtgggtgtcaaaactgaggatttggtgaaaatcattctaaaacaacctcaaatcttagggtatacaattgagaataacataaaaccacatattgactttttgagaggcttgggggtgcctgattcccggttaggacaaataataacagcaaatccatctttcttttcttatagct
tggagttgtctctgaagccaaaggtaagatttttaaccgaggaagttggcattaaaagaacagacttggggaaagttgtgattctaggccctgagatactgagacaacctgctgaagccttgaaatctcggttagaatttctttcaaaggagcttggagcatcaaagggaaatctagtgaaaatggtcacaaagcatcca
cagcttctccactacagcattaccgatggtatacagccacgaatcaattttttgaggagcattggcatgaatgaggctgacattgtgaaagttttaacaagattaccccagattttgtctctgtcagtggagaagaatctgcgccccaaatatttgtatttagtcaaagaactcgaaaatggagttgagtcattatcagc
acaccccttatatttcagcatatcgcttaaacaacgcatttggcctcgtcacagattcttgacttccctgaaaaaggttacaaacagacctttccctataaaagccttacttgttaatgatgactgtttctgtaagcggtgggctgatacaactcttcaagattaccaggcatttcgacaattgttactgggtgagttgg
caggggaggtttcacagaagcagggcgttgacatgtgattaaatatggagcatacaaaatagcattacatttgcaggtgctgacatcaaactgtgtactgatggtagtctacagaaaccattgcgagatgaaccttctgagatagaagcgttgttggaaacagaaagcctattgcattctgaataagcctcccagaatct
caaaattctaagtaatgatattgaatcataaccatggtgatacccttctgaaagtatccttacattcgcgaccgttttatccaaagttggaagttgtaacattgatgctaattggtaagttcattgcaagtcttactaaacaatttctatatttctgtgacatcaaacagtggaaaatcttgacattatatcttaaattt
gtgacaccaaaaggtattttattctacatgctgactggtgtttggttctgtgtttcagGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTA
GATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTGTTAAAATATT
GATTTCTCGCAATGTTGAAAAAGTCGGCATCGACAAAAAGTCGGCAAGGGTCCTGAATACAACTTCTCGGCAACATCG

Intron 15 GTAAAACTTG ... GTTTCTAGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	53.85	24	16	28
A2	44.27	26.5	2.3	21
A3	43.18	50	6.1	38
A4	50	35	2.7	35
A5	53.85	18	2.9	21
A6	41.69	71.3	2.6	51
A7	48.03	79	5.7	73
A8	52.78	51	2	57
A9	40.77	77	8.7	53
A10	44.51	86	12.8	69

>TRINITY_DN109840_c1_g1_i7 from sample A2 / Example spliced isoform

CACTGGTAAAAATAAATCCAGGTTACGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGAGAGAGATAAATCTTTATATGGCGACACGTTAAAGACTCAAGAACGGCG
ACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCCTACGTTTGGACTCTTGT
GGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAATTGCTATCATGACGATGC
CGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAAAGCAAATGTTCTTCAAA
AGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAATCTCCTAAATCTGAAAAC
ATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCACTTTGCCCGAATTTATAA
TAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGTGCCTGATTCCCGGTTAG
GACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTCTTTCAAAGGAGCTTGGA
GCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGGTGATTTTTCATTTCTCCAGCTGATTTATTTGAGGTTTTCAATGCGT
AAGGTATACTTCCATATTCCTAAGCATATATCAATTATTTCCCATATTCCTAAGCATATGAAATGTATGCTTTTGTTTCTCTGTACACCGAGGTTGACAATATTATTCATTCTAAGCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCGAAAATGGAGTTGAGTCA
TTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTTCGACAATTGTTACTGGG
TGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGCATTCTGAATAAGCCTCC
CAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTTCAGTTTCGAACCAGGAC
TTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTCAAATCAGGAAGATAATC
CTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTG

>TRINITY_DN109840_c1_g1_i8 from sample A2 / Example unspliced isoform:

CACTGGTAAAAATAAATCCAGGTTACGACGAAATGACATCTGGTGTTGGAGTTGCTTGAAGAAAATCTTTAAGCCGAGGTCAATTCCATTGGCATCAGTTAAGAGAGCGGAAAAGTAGCGGAATGAATCTTCTGCTTGAAATTTTTAGCCGgtaaaacttgtttttatctaaatttttagtttctgaacggtggtgaatc
gattttccgttaattaaaattcacagcactctgaaaaacttcttaaaccctgactctggttgcgggcgggaaaatctttattccgcctttgagattgttgaagctgtaaatttctaatttgctcggggattttgtcaaaataatgcccggaatcatctgtttctagagAGAGAGATAAATCTTTATATGGCGACACGTTA
AAGACTCAAGAACGGCGACCAAGGAGGTGCCGGCCGAGGAATCGAACACGGGACCCGCTGCTTTAGGTCCTACGTGCTTTAAGAATGGCGAGAAGGAAGATTTCAGAAAGAATAGAACACGGGACACGAATCTTTAGGGCGTATATGCTATTTTGAAGGTGCCTGTCTTATATTTTTCGAAATGTTACCTGCTACTTGCC
TACGTTTGGACTCTTGTGGAAGAAGAGGATTCCAATACCCCGCTCTTTCGTCTTTATACTTGAAAGATTATGTATTGCCTTTGAGAATGAATACATTTTTTCGAAGAAAGCGTTGTTTTGTTCTGTGTATACGCCGTTCAAATCTTGGGGCGTTGAAATCCAACCGGTGCCGCTCGGGGAACCGTTATCCACGATGCAAT
TGCTATCATGACGATGCCGATGACTTTGAGGATGACGAAGACTACGGTACTATTGACAGTGATGTGCTTCTACCTGGGGAACACACTTATGTGGATGCTGATAATGCCAAGTCTGCAGAAACAACCTTTTCTTCCACGTCACTGGGTGCATTCTCAGGACAATCCTTCCATGAACAAGAACTGAAGCAAGGAAAAACAAA
AGCAAATGTTCTTCAAAAGACTGGAAAGAGGTTGGCTAGGAATGGTACGGTGAGGGTTAATTCATTGGGCCTGCACCCTTCCCCTTTGAGGCTACCTCGAAATGAGTGGGAGAAGAGAGCCTTTGAGATCATACGGCAGCAGAAATTAAGAAATATTGAACTAGAAAGGAAGCGAAGCGAGCAGAAAATATTGCTTGAAT
CTCCTAAATCTGAAAACATTGACCAGATTATAGAAAGTTCCCAGAGATTAGGCTCCACGAATGCAAACTTGAATTATGAGGTTACAGCTGGAAACATTGAGGATGTTGAATATCAATTGATGGCAAAGCGATTAGGTTTTGAAGCAAAATGGAAACCCTTGATTCAGTATTTGAGTAGCCTTGGCTTAAATGAGTGTCAC
TTTGCCCGAATTTATAATAGGCACAAACCTACCCTAAGAACAAAAGTATCATCAGCCCAGGAAAGATTGGATTTCTTACAAAGTGTGGGTGTCAAAACTGAGGATTTGGTGAAAATCATTCTAAAACAACCTCAAATCTTAGGGTATACAATTGAGAATAACATAAAACCACATATTGACTTTTTGAGAGGCTTGGGGGT
GCCTGATTCCCGGTTAGGACAAATAATAACAGCAAATCCATCTTTCTTTTCTTATAGCTTGGAGTTGTCTCTGAAGCCAAAGGTAAGATTTTTAACCGAGGAAGTTGGCATTAAAAGAACAGACTTGGGGAAAGTTGTGATTCTAGGCCCTGAGATACTGAGACAACCTGCTGAAGCCTTGAAATCTCGGTTAGAATTTC
TTTCAAAGGAGCTTGGAGCATCAAAGGGAAATCTAGTGAAAATGGTCACAAAGCATCCACAGCTTCTCCACTACAGCATTACCGATGGTATACAGCCACGAATCAATTTTTTGAGGAGCATTGGCATGAATGAGGCTGACATTGTGAAAGTTTTAACAAGATTACCCCAGGTGATTTTTCATTTCTCCAGCTGATTTATT
TGAGGTTTTCAATGCGTAAGGTATACTTCCATATTCCTAAGCATATATCAATTATTTCCCATATTCCTAAGCATATGAAATGTATGCTTTTGTTTCTCTGTACACCGAGGTTGACAATATTATTCATTCTAAGCAGATTTTGTCTCTGTCAGTGGAGAAGAATCTGCGCCCCAAATATTTGTATTTAGTCAAAGAACTCG
AAAATGGAGTTGAGTCATTATCAGCACACCCCTTATATTTCAGCATATCGCTTAAACAACGCATTTGGCCTCGTCACAGATTCTTGACTTCCCTGAAAAAGGTTACAAACAGACCTTTCCCTATAAAAGCCTTACTTGTTAATGATGACTGTTTCTGTAAGCGGTGGGCTGATACAACTCTTCAAGATTACCAGGCATTT
CGACAATTGTTACTGGGTGAGTTGGCAGGGGAGGTTTCACAGAAGCAGGGCGTTGACATGTGATTAAATATGGAGCATACAAAATAGCATTACATTTGCAGGTGCTGACATCAAACTGTGTACTGATGGTAGTCTACAGAAACCATTGCGAGATGAACCTTCTGAGATAGAAGCGTTGTTGGAAACAGAAAGCCTATTGC
ATTCTGAATAAGCCTCCCAGAATCTCAAAATTCTAAGTAATGATATTGAATCATAACCATGGTGATACCCTTCTGAAAGTATCCTTACATTCGCGACCGTTTTATCCAAAGTTGGAAGTTGTAACATTGATGCTAATTGGCTGTCAGCTAGACTGCAGTGTTTACTGCTTGTTAGTGATTTTTTGCCCTATTATGCTGTT
CAGTTTCGAACCAGGACTTCAGATATCTATTTAAAGAAGGAACTTCATGGAGTCATTGCAAAGCAACACAATATGGAATTAGATGTAAACCATACCTCATGGGATAGGTGAAATTGATTATGTAATATTGACCCGAAAATGGAAAAGGAAGCACTCAGGATCAATTTTTCAAAGCTGTCTTTTGTCAGCGTTATATTTTC
AAATCAGGAAGATAATCCTCAAAACAGTGTATTCTCCGTCCATAACCCCAGTTCGATTTTTTAGTTTGCTG