NA ----> NA

Intron 1 GTAAGTCTTT ... TTCTTACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	26.92	61.1	5	22
A2	34.78	38	0	20
A3	31.19	44.7	0	20
A4	33.93	24.1	0	12
A5	31.41	17.9	0	8
A6	51.19	6.7	2	7
A7	39.06	17.3	0	11
A8	-1	0	0	0
A9	20.71	3.9	0	1
A10	0	5.3	0	0

>TRINITY_DN132627_c3_g1_i20 from sample A1 / Example spliced isoform

CTAAACTTTGCGTCTAAAGAGTTTAGCAAGGTTTAAGCTCTGAAATAACATTTAGAAAGCAACTTGCCCATTTTCGTTGAATGCAGCCATGGCCATGGCTACGGCAGATGCATTATTGCAGGCGTTGCACAGCATTCCACTGGGGGCGGTTCCAGGACTTGTTGACGCTCTTCTCCTCTCAGCTGGTCTGCACTCTTCAG
TTCTTCTCAATCACCTCATCTACACTTTTCCACCACTTCTGAAGGATCATCTCAAGGAGGATCAACAATTTACTTTGGATGCAAAAGAACATAAATTTCTACTAGCTTTTGTTTCAACAGTTACACATCTATTCAAGAAACCAGAAAGTGATATGGGTGCACTGAAAGCACTTATCTGGATAGTGTATTTCCCAATATTG
AAAAGGACTTCCGTTGAAAACTTTGTTTTGCATAATCAGGTTGCAGAGGCATTGGCTACAATTGCCATTGAAAGACATTCTTGGGGTGACATGGAAGCGACCCTGCTACCGTACTGTTTGACATCAGTGGTATCTTCTGTTGCTTCTGAGCTGCAAGTCCTTTCATCGTCTGATTTGCAAGATGATGCCTACCCATTGAG
TTTGGAAATCATAACCTCTTTGAGATCTTTAGACCTAAATCAGGAACATTTAGAACTCGCAAATAGGTTTTTACCATGCCCTGTAGCATGCCAGCTATTGGCAACATTATTGCTGGCAGCTTTGAAGGTATTGAGTTCAAATGAGGTTGGAATGCCACTGAAGGAGATGTATGAGAGGGTTAACTCGTCTGCAGGGAAAT
TTGCTAGGCAGATGGTTTCAGATCTCTTGGACCCAGCGTTAAACATGCTTTCACAATGTTCAGATTATAAAGTGCGGCAGTGTGCAATGACCGTGCTTTTACCACCTATCTTGCAGACAGTAGATATACTTGCATCATTTGAAGCTTGTTCTTCTGGGCAACTATCTGACAATTCCAGGGTACTTGTCATGCAGAAGGTA
TGGAGCTGCTTGAAGTGTTTGTTTTCTCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGATGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTAGAGCAGGTTTGGTTGA
TGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATGAAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGATAGATGGGCTGACA
TGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAGATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCCCTGGAATCCGGCAT
ACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAAACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTTGTTCTGGGTCCATT
TATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTAATGGCTC
TAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTTCAACCCA
AAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAATTATGCACTGGTTCAATTTGCAGGGCACCACATATTCAAATAAACCTCTTTT
CACTCATCAAGAATGGATTGCAAATAACCTGTGCAACTTTGCTGAGAGCTTTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCATGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCCTTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACTCATTCAGGTGGTTC
AGAATCATGCATTTGAAATTTCAAAACGTGTGTATAACTCAAGCTGCATGCCTGATAAGTTGCTACTTCTCATTTTAAGTCTACTGAAAGAATGTCAACCTCGAAAGCAATTTTCCAATAATATGAAAGGTTGCACAATGAAACATGAGAGAAAACAAGCATTAGTAGAGTTTGATGGAAAGGAGGATTTACCGGGATAC
TGTACACTTGTCACAAATATTTCTGATGTTATCCTTTCTATAATGGGGGAACTTATTTCATATGCAAGGTCAACATTCACAATATTTTGGTCTGCTGATTTCTCATGGGATGGGCCATTACCTGGTTCAGTAACTGGAAAACTTGGTGGACCAAGTCAACGGCGACTTCCATCTTCTGCAACTTCAGTAGTCCTGCAAGC
AATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGG
CTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGTGGTGTTGCTTGGATTCTTTCTTG
TCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAGCGAGTGCCTTCTGA
TGGTAGTCTTCACAACCAAAAGAAAGTTGAGATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCTCTGAAGTGGTTCC
TTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATGTAGCAGCCAGA
GAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATATGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAAATGTTTCTTTTGGA
GCTTATAGATTCTGTGGTCAATGATGTGGACCTTGCCAGGGAACTGTACAAAAAGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCATAAATGCCTTCATATGAACAACTTGCCTGCAGTTCGCCAGT
ATATTGAAATCTTTGCTATGCAATTATACTTAAAGTTTCCATCCATGATAGTGAAGCAAATGACTCCAATATTGTATGATTACAGTATGAAGCCACAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCTCCAGTTTGAGCTCCTGGAGGAGTTGCTTCCTCCATTGCTT
CCATTTTTGACTTCACATCACCACAGTTTGCGTGGCTTCTCTCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGGTTGAGATCTTCAGT
GGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGATGCTGTAACTC
TTAAGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCATCAATACCAAA
TTGGCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACTTGTGAGGTCTT
TAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTATACCACTTAATA
AGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAATATAGATTTTC
TTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCGGATATCTGTTCTAG
GCTTATTATGGTTCTGCCAGATAACACATGAAGGGTGAGCAAGTGAATACAAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGCAGCAGACAGGAAGG
AGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGATGGCTTCTATTCCA
GAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTAAGATAGTCATGAGA
AAGTTTCCCTAACTC

>TRINITY_DN132627_c3_g1_i9 from sample A1 / Example unspliced isoform:

GAAGAACTTAGAGCAGGTTTGgtaagtctttagttagaatggaacatgcaaatgtatttaaattggaaagcagctatctattgtctaaagaggatttataacaatttaccttatgatgttttcgtctttacaaatttcttaccagGTTGATGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTT
TAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATGAAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGATAGATGGGCTGACATGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAG
GTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAGATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCCCTGGAATCCGGCATACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATT
CTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAAACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTTGTTCTGGGTCCATTTATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAG
GCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTAATGGCTCTAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGAT
AACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTTCAACCCAAAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCT
AGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAATTATGCACTGGTTCAATTTGCAGGGCACCACATATTCAAATAAACCTCTTTTCACTCATCAAGAATGGATTGCAAATAACCTGTGCAACTTTGCTGAGAGCT
TTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCATGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCCTTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACTCATTCAGGTGGTTCAGAATCATGCATTTGAAATTTCAAAACGTGTGTATAACTCAAGCTGCATG
CCTGATAAGTTGCTACTTCTCATTTTAAGTCTACTGAAAGAATGTCAACCTCGAAAGCAATTTTCCAATAATATGAAAGGTTGCACAATGAAACATGAGAGAAAACAAGCATTAGTAGAGTTTGATGGAAAGGAGGATTTACCGGGATACTGTACACTTGTCACAAATATTTCTGATGTTATCCTTTCTATAATGGGGGA
ACTTATTTCATATGCAAGGTCAACATTCACAATATTTTGGTCTGCTGATTTCTCATGGGATGGGCCATTACCTGGTTCAGTAACTGGAAAACTTGGTGGACCAAGTCAACGGCGACTTCCATCTTCTGCAACTTCAGTAGTCCTGCAAGCAATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATT
TGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGT
TTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGTGGTGTTGCTTGGATTCTTTCTTGTCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGA
TGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAGCGAGTGCCTTCTGATGGTAGTCTTCACAACCAAAAGAAAGTTGAGATTATGTGGTCATTGGTGC
AATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCTCTGAAGTGGTTCCTTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTC
TCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATGTAGCAGCCAGAGAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATA
TGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAAATGTTTCTTTTGGAGCTTATAGATTCTGTGGTCAATGATGTGGACCTTGCCAGGGAACTGTACA
AAAAGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCATAAATGCCTTCATATGAACAACTTGCCTGCAGTTCGCCAGTATATTGAAATCTTTGCTATGCAATTATACTTAAAGTTTCCATCCATGATA
GTGAAGCAAATGACTCCAATATTGTATGATTACAGTATGAAGCCACAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCTCCAGTTTGAGCTCCTGGAGGAGTTGCTTCCTCCATTGCTTCCATTTTTGACTTCACATCACCACAGTTTGCGTGGCTTCTCTCAGATTTT
AGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGGTTGAGATCTTCAGTGGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGG
GACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGATGCTGTAACTCTTAAGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCA
GACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCATCAATACCAAATTGGCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGA
GGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACTTGTGAGGTCTTTAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAAC
AGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTATACCACTTAATAAGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAG
GGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAATATAGATTTTCTTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAA
AAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCGGATATCTGTTCTAGGCTTATTATGGTTCTGCCAGATAACACATGAAGGGTGAGCAAGTGAATAC
AAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGCAGCAGACAGGAAGGAGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATT
AGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGATGGCTTCTATTCCAGAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAG
GTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTAAGATAGTCATGAGAAAGTTTCCCTAACTC

Intron 2 GTAGTCTTCA ... GAAAGTTGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	87.3	4	27	28
A2	67.8	19	39	41
A3	56.67	26	37	31
A4	65.52	15	24	33
A5	74.36	5	15	14
A6	66.67	9	20	16
A7	65.22	16	25	35
A8	100	0	18	18
A9	63.64	26	48	43
A10	59.09	9	16	10

>TRINITY_DN116618_c3_g1_i18 from sample A3 / Example spliced isoform

ACCAGAGCAGGACTAAACTTTGCGTCTAAAGAGTTTAGCAAGGTTTAAGCTCTGAAATAACATTTAGAAAGCAACTTGCCCATTTTCGTTGAATGCAGCCATGGCCATGGCTACGGCAGATGCATTATTGCAGGCGTTGCACAGCATTCCACTGGGGGCGGTTCCAGGACTTGTTGACGCTCTTCTCCTCTCAGCTGGTC
TGCACTCTTCAGTTCTTCTCAATCACCTCATCTACACTTTTCCACCACTTCTGAAGGATCATCTCAAGGAGGATCAACAATTTACTTTGGATGCAAAAGAACATAAATTTCTACTAGCTTTTGTTTCAACAGTTACACATCTATTCAAGAAACCAGAAAGTGATATGGGTGCACTGAAAGCACTTATCTGGATAGTGTAT
TTCCCAATATTGAAAAGGACTTCCGTTGAAAACTTTGTTTTGCATAATCAGGTTGCAGAGGCATTGGCTACAATTGCCATTGAAAGACATTCTTGGGGTGACATGGAAGCGACCCTGCTACCGTACTGTTTGACATCAGTGGTATCTTCTGTTGCTTCTGAGCTGCAAGTCCTTTCATCGTCTGATTTGCAAGATGATGC
CTACCCATTGAGTTTGGAAATCATAACCTCTTTGAGATCTTTAGACCTAAATCAGGAACATTTAGAACTCGCAAATAGGTTTTTACCATGCCCTGTAGCATGCCAGCTATTGGCAACATTATTGCTGGCAGCTTTGAAGGTATTGAGTTCAAATGAGGTTGGAATGCCACTGAAGGAGATGTATGAGAGGGTTAACTCGT
CTGCAGGGAAATTTGCTAGGCAGATGGTTTCAGATCTCTTGGACCCAGCGTTAAACATGCTTTCACAATGTTCAGATTATAAAGTGCGGCAGTGTGCAATGACCGTGCTTTTACCACCTATCTTGCAGACAGTAGATATACTTGCATCATTTGAAGCTTGTTCTTCTGGGCAACTATCTGACAATTCCAGGAGATGGGAG
CTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGA
AGTCGTCGAGCAATTTTACTACACTATAAGGTACTTGTCATGCAGAAGGTATGGAGCTGCTTGAAGTGTTTGTTTTCTCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGA
TGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTAGAGCAGGTTTGGTTGATGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATG
AAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGATAGATGGGCTGACATGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAG
ATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCCCTGGAATCCGGCATACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAA
ACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTTGTTCTGGGTCCATTTATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATT
TGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTAATGGCTCTAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTG
GTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTTCAACCCAAAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAAT
TATGCACTGGTTCAATTTGCAGGGCACCACATATTCAAATAAACCTCTTTTCACTCATCAAGAATGGATTGCAAATAACCTGTGCAACTTTGCTGAGAGCTTTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCATGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCC
TTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACTCATTATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTT
GGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAAT
TTTACTACACTATAAGTGGTGTTGCTTGGATTCTTTCTTGTCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGAT
GGGTGATGAATTGGGGTTTGTTAAAGCGAGTGCCTTCTGATGATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCTCT
GAAGTGGTTCCTTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATG
TAGCAGCCAGAGAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATATGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAAATG
TTTCTTTTGGAGCTTATAGATTCTGTGGTCAATGATGTGGACCTTGCCAGGGAACTGTACAAAAAGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCATAAATGCCTTCATATGAACAACTTGCCTGC
AGTTCGCCAGTATATTGAAATCTTTGCTATGCAATTATACTTAAAGTTTCCATCCATGATAGTGAAGCAAATGACTCCAATATTGTATGATTACAGTATGAAGCCACAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCTCCAGTTTGAGCTCCTGGAGGAGTTGCTTC
CTCCATTGCTTCCATTTTTGACTTCACATCACCACAGTTTGCGTGGCTTCTCTCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGGTTG
AGATCTTCAGTGGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGA
TGCTGTAACTCTTAAGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCA
TCAATACCAAATTGGCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACT
TGTGAGGTCTTTAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTAT
ACCACTTAATAAGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAA
TATAGATTTTCTTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCGGAT
ATCTGTTCTAGGCTTATTATGGTTCTGCCAGATAACACATGAAGGGTGAGCAAGTGAATACAAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGCAGC
AGACAGGAAGGAGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGATGG
CTTCTATTCCAGAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTA

>TRINITY_DN116618_c3_g1_i24 from sample A3 / Example unspliced isoform:

ACCAGAGCAGGACTAAACTTTGCGTCTAAAGAGTTTAGCAAGGTTTAAGCTCTGAAATAACATTTAGAAAGCAACTTGCCCATTTTCGTTGAATGCAGCCATGGCCATGGCTACGGCAGATGCATTATTGCAGGCGTTGCACAGCATTCCACTGGGGGCGGTTCCAGGACTTGTTGACGCTCTTCTCCTCTCAGCTGGTC
TGCACTCTTCAGTTCTTCTCAATCACCTCATCTACACTTTTCCACCACTTCTGAAGGATCATCTCAAGGAGGATCAACAATTTACTTTGGATGCAAAAGAACATAAATTTCTACTAGCTTTTGTTTCAACAGTTACACATCTATTCAAGAAACCAGAAAGTGATATGGGTGCACTGAAAGCACTTATCTGGATAGTGTAT
TTCCCAATATTGAAAAGGACTTCCGTTGAAAACTTTGTTTTGCATAATCAGGTTGCAGAGGCATTGGCTACAATTGCCATTGAAAGACATTCTTGGGGTGACATGGAAGCGACCCTGCTACCGTACTGTTTGACATCAGTGGTATCTTCTGTTGCTTCTGAGCTGCAAGTCCTTTCATCGTCTGATTTGCAAGATGATGC
CTACCCATTGAGTTTGGAAATCATAACCTCTTTGAGATCTTTAGACCTAAATCAGGAACATTTAGAACTCGCAAATAGGTTTTTACCATGCCCTGTAGCATGCCAGCTATTGGCAACATTATTGCTGGCAGCTTTGAAGGTATTGAGTTCAAATGAGGTTGGAATGCCACTGAAGGAGATGTATGAGAGGGTTAACTCGT
CTGCAGGGAAATTTGCTAGGCAGATGGTTTCAGATCTCTTGGACCCAGCGTTAAACATGCTTTCACAATGTTCAGATTATAAAGTGCGGCAGTGTGCAATGACCGTGCTTTTACCACCTATCTTGCAGACAGTAGATATACTTGCATCATTTGAAGCTTGTTCTTCTGGGCAACTATCTGACAATTCCAGGAGATGGGAG
CTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGA
AGTCGTCGAGCAATTTTACTACACTATAAGGTACTTGTCATGCAGAAGGTATGGAGCTGCTTGAAGTGTTTGTTTTCTCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGA
TGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTAGAGCAGGTTTGGTTGATGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATG
AAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGATAGATGGGCTGACATGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAG
ATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCCCTGGAATCCGGCATACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAA
ACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTTGTTCTGGGTCCATTTATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATT
TGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTAATGGCTCTAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTG
GTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTTCAACCCAAAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAAT
TATGCACTGGTTCAATTTGCAGGGCACCACATATTCAAATAAACCTCTTTTCACTCATCAAGAATGGATTGCAAATAACCTGTGCAACTTTGCTGAGAGCTTTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCATGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCC
TTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACTCATTATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTT
GGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAAT
TTTACTACACTATAAGTGGTGTTGCTTGGATTCTTTCTTGTCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGAT
GGGTGATGAATTGGGGTTTGTTAAAGCGAGTGCCTTCTGATGgtagtcttcacaaccaaaagaaagttgagATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCAT
GATGGTGGAAGTAATAGACCAGGACCTCTGAAGTGGTTCCTTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGA
TCTGGATGGGGAGTTGCTTGAAAACTATGTAGCAGCCAGAGAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATATGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATG
TCCTGCCTGCATTTAGTTCTGGGAAAATGTTTCTTTTGGAGCTTATAGATTCTGTGGTCAATGATGTGGACCTTGCCAGGGAACTGTACAAAAAGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCAT
AAATGCCTTCATATGAACAACTTGCCTGCAGTTCGCCAGTATATTGAAATCTTTGCTATGCAATTATACTTAAAGTTTCCATCCATGATAGTGAAGCAAATGACTCCAATATTGTATGATTACAGTATGAAGCCACAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCT
CCAGTTTGAGCTCCTGGAGGAGTTGCTTCCTCCATTGCTTCCATTTTTGACTTCACATCACCACAGTTTGCGTGGCTTCTCTCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATT
TGGAGGGAAATGCTGATTGTACAAGGTTGAGATCTTCAGTGGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGA
GGGGAGCTGCGGGTTGCCATGGAAGAAGATGCTGTAACTCTTAAGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAA
AATCCTTTCTCATAGGTTTGATGAAAGCATCAATACCAAATTGGCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCA
TTCCTAATCTTGCAGGATTGGCACGAACTTGTGAGGTCTTTAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATT
TTGGGATTGGAGCAGACAGCAAACAGTATACCACTTAATAAGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGA
ATATACTCGGCAGCATCATCAGGAGTAAATATAGATTTTCTTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGC
TCTCTGTTGGAGGACAAGGGCAATCGGATATCTGTTCTAGGCTTATTATGGTTCTGCCAGATAACACATGAAGGGTGAGCAAGTGAATACAAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGA
GGAGCAGTGCTGAAGCAATTGCTGGCAGCAGACAGGAAGGAGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAA
CAGAAATATGTGTGTGGATACCCTGATGGCTTCTATTCCAGAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGA
GGAATATTCTTATGACAGATTTTGTA

Intron 3 GTAGTACTTT ... AATGATGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	36.36	7	2	6
A2	33.33	11	2	9
A3	43.75	9	3	11
A4	21.21	26	6	8
A5	42.86	2	1	2
A6	20	4	1	1
A7	23.08	10	3	3
A8	24.44	17	6	5
A9	20	12	2	4
A10	25	3	2	0

>TRINITY_DN106972_c0_g2_i1 from sample A4 / Example spliced isoform

GGACCAGAGCAGGACTAAACTTTGCGTCTAAAGAGTTTAGCAAGGTTTAAGCTCTGAAATAACATTTAGAAAGCAACTTGCCCATTTTCGTTGAATGCAGCCATGGCCATGGCTACGGCAGATGCATTATTGCAGGCGTTGCACAGCATTCCACTGGGGGCGGTTCCAGGACTTGTTGACGCTCTTCTCCTCTCAGCTGG
TCTGCACTCTTCAGTTCTTCTCAATCACCTCATCTACACTTTTCCACCACTTCTGAAGGATCATCTCAAGGAGGATCAACAATTTACTTTGGATGCAAAAGAACATAAATTTCTACTAGCTTTTGTTTCAACAGTTACACATCTATTCAAGAAACCAGAAAGTGATATGGGTGCACTGAAAGCACTTATCTGGATAGTGT
ATTTCCCAATATTGAAAAGGACTTCCGTTGAAAACTTTGTTTTGCATAATCAGGTTGCAGAGGCATTGGCTACAATTGCCATTGAAAGACATTCTTGGGGTGACATGGAAGCGACCCTGCTACCGTACTGTTTGACATCAGTGGTATCTTCTGTTGCTTCTGAGCTGCAAGTCCTTTCATCGTCTGATTTGCAAGATGAT
GCCTACCCATTGAGTTTGGAAATCATAACCTCTTTGAGATCTTTAGACCTAAATCAGGAACATTTAGAACTCGCAAATAGGTTTTTACCATGCCCTGTAGCATGCCAGCTATTGGCAACATTATTGCTGGCAGCTTTGAAGGTATTGAGTTCAAATGAGGTTGGAATGCCACTGAAGGAGATGTATGAGAGGGTTAACTC
GTCTGCAGGGAAATTTGCTAGGCAGATGGTTTCAGATCTCTTGGACCCAGCGTTAAACATGCTTTCACAATGTTCAGATTATAAAGTGCGGCAGTGTGCAATGACCGTGCTTTTACCACCTATCTTGCAGACAGTAGATATACTTGCATCATTTGAAGCTTGTTCTTCTGGGCAACTATCTGACAATTCCAGGGTACTTG
TCATGCAGAAGGTATGGAGCTGCTTGAAGTGTTTGTTTTCTCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGATGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTAGA
GCAGGTTTGGTTGATGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATGAAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGA
TAGATGGGCTGACATGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAGATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCC
CTGGAATCCGGCATACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAAACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTT
GTTCTGGGTCCATTTATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGT
TGGGCTAATGGCTCTAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAAC
AACACTTCAACCCAAAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAATTATGCACTGGTTCAATTTGCAGGGCACCACATATTCA
AATAAACCTCTTTTCACTCATCAAGAATGGATTGCAAATAACCTGTGCAACTTTGCTGAGAGCTTTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCATGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCCTTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACT
CATTCAGGTGGTTCAGAATCATGCATTTGAAATTTCAAAACGTGTGTATAACTCAAGCTGCATGCCTGATAAGTTGCTACTTCTCATTTTAAGTCTACTGAAAGAATGTCAACCTCGAAAGCAATTTTCCAATAATATGAAAGGTTGCACAATGAAACATGAGAGAAAACAAGCATTAGTAGAGTTTGATGGAAAGGAGG
ATTTACCGGGATACTGTACACTTGTCACAAATATTTCTGATGTTATCCTTTCTATAATGGGGGAACTTATTTCATATGCAAGGTCAACATTCACAATATTTTGGTCTGCTGATTTCTCATGGGATGGGCCATTACCTGGTTCAGTAACTGGAAAACTTGGTGGACCAAGTCAACGGCGACTTCCATCTTCTGCAACTTCA
GTAGTCCTGCAAGCAATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGT
TTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGTGGTGTTGCT
TGGATTCTTTCTTGTCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAG
CGAGTGCCTTCTGATGGTAGTCTTCACAACCAAAAGAAAGTTGAGATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACC
TCTGAAGTGGTTCCTTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACT
ATGTAGCAGCCAGAGAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATATGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAA
ATGTTTCTTTTGGAGCTTATAGATTCTGTGGTCAATGATGTGGACCTTGCCAGGGAACTGTACAAAAAGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCATAAATGCCTTCATATGAACAACTTGCC
TGCAGTTCGCCAGTATATTGAAATCTTTGCTATGCAATTATACTTAAAGTTTCCATCCATGATAGTGAAGCAAATGACTCCAATATTGTATGATTACAGTATGAAGCCACAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCTCCAGTTTGAGCTCCTGGAGGAGTTGC
TTCCTCCATTGCTTCCATTTTTGACTTCACATCACCACAGTTTGCGTGGCTTCTCTCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGG
TTGAGATCTTCAGTGGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGA
AGATGCTGTAACTCTTAAGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAA
GCATCAATACCAAATTGGCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGA
ACTTGTGAGGTCTTTAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAG
TATACCACTTAATAAGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGT
AAATATAGATTTTCTTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCG
GATATCTGTTCTAGGCTTATTATGGTTCTGCCAGATAACACATGAAGGGTGAGCAAGTGAATACAAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGC
AGCAGACAGGAAGGAGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGA
TGGCTTCTATTCCAGAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTA
AGATAGTCATGAGAAAGTTTCC

>TRINITY_DN106972_c0_g2_i13 from sample A4 / Example unspliced isoform:

CTTTCATATACTCATGAACAAACTTTTCTTTGCTTCTATATTGTTAAATTCTTCTCAATTTGGAATCTGGATATCCCCTGATATTGCAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCTCCAGTTTGAGCTCCTGGAGGAGTTGCTTCCTCCATTGCTTCCATTTTTG
ACTTCACATCACCACAGTTTGCGTGGCTTCTCTCAGgtagtactttggtaatgttgatgttgaggtttgtattgcattagagaaggtatgatcttggtgctttggaaagaagtttcgggttctcatatatattgtccttgaatgatgcagATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCC
TATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGGTTGAGATCTTCAGTGGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGC
TCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGATGCTGTAACTCTTAAGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACT
GATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCATCAATACCAAATTGGCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAA
AGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACTTGTGAGGTCTTTAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATAC
AAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTATACCACTTAATAAGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAA
ATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAAT

Intron 4 GTTGAGATCT ... ACACTAGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	60.98	8	13	12
A2	78.26	5	23	13
A3	65.38	9	13	21
A4	73.68	5	16	12
A5	61.9	4	7	6
A6	63.64	4	6	8
A7	69.23	8	12	24
A8	65.96	8	10	21
A9	60.98	16	26	24
A10	61.27	12	16	22

>TRINITY_DN46312_c0_g1_i9 from sample A7 / Example spliced isoform

TCAGGTAGTACTTTGGTAATGTTGATGTTGAGGTTTGTATTGCATTAGAGAAGGTATGATCTTGGTGCTTTGGAAAGAAGTTTCGGGTTCTCATATATATTGTCCTTGAATGATGCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGG
AGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACG
AACTTGTGAGGTCTTTAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACA
GTATACCACTTAATAAGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAG
TAAATATAGATTTTCTTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATC
GGATATCTGTTCTAGGCTTATTATGGTTCTGCCAGATAACACATGAAGGGTGAGCAAGTGAATACAAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGG
CAGCAGACAGGAAGGAGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTG
ATGGCTTCTATTCCAGAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGT
AAGATAGTCATGAGAAAGTTTCCCTAACTCCAATTTTTTCTTCCACA

>TRINITY_DN46312_c0_g1_i10 from sample A7 / Example unspliced isoform:

CGTACATCAAACACATTAGAACAAATTTCATCTCCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGATGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTAGAGCAGGTT
TGGTTGATGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATGAAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGATAGATGG
GCTGACATGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAGATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCCCTGGAAT
CCGGCATACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAAACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTTGTTCTGG
GTCCATTTATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTA
ATGGCTCTAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTT
CAACCCAAAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAATTATGCACTGGTTCAATTTGCAGGGCACCACATATTCAAATAAAC
CTCTTTTCACTCATCAAGAATGGATTGCAAATAACCTGTGCAACTTTGCTGAGAGCTTTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCATGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCCTTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACTCATTCAG
GTGGTTCAGAATCATGCATTTGAAATTTCAAAACGTGTGTATAACTCAAGCTGCATGCCTGATAAGTTGCTACTTCTCATTTTAAGTCTACTGAAAGAATGTCAACCTCGAAAGCAATTTTCCAATAATATGAAAGGTTGCACAATGAAACATGAGAGAAAACAAGCATTAGTAGAGTTTGATGGAAAGGAGGATTTACC
GGGATACTGTACACTTGTCACAAATATTTCTGATGTTATCCTTTCTATAATGGGGGAACTTATTTCATATGCAAGGTCAACATTCACAATATTTTGGTCTGCTGATTTCTCATGGGATGGGCCATTACCTGGTTCAGTAACTGGAAAACTTGGTGGACCAAGTCAACGGCGACTTCCATCTTCTGCAACTTCAGTAGTCC
TGCAAGCAATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAA
GCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGTGGTGTTGCTTGGATTC
TTTCTTGTCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAGCGAGTGC
CTTCTGATGGTAGTCTTCACAACCAAAAGAAAGTTGAGATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCCCTGAAG
TGGTTCCTTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATGTAGC
AGCCAGAGAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATATGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAAATGTTTC
TTTTGGAGCTTATAGATTCTGTGGTCAATGATGTGGACCTTGCCAGGGAACTGTACAAAAAGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCATAAATGCCTTCATATGAACAACTTGCCTGCAGTT
CGCCAGTATATTGAAATCTTTGCTATGCAATTATACTTAAAGTTTCCATCCATGATAGTGAAGCAAATGACTCCAATATTGTATGATTACAGTATGAAGCCACAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCTCCAGTTTGAGCTCCTGGAGGAGTTGCTTCCTCC
ATTGCTTCCATTTTTGACTTCACATCACCACAGTTTGCGTGGCTTCTCTCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGgttgagat
cttcagtggagaaacacttggatgtatttgatcctgttgcttcagcaacaccacggggactattctgtttcaaaaatggcgatactgacccatctactgagctcccttttgagcgcgttccagtttctattgtagaacatgtgatagactttctcaatggggtcagaggggagctgcgggttgccatggaagaagatgct
gtaactcttaagaatgaagaacttagaagcatgaccaaccatgacaatctatattcagacatgcaggaaggaaatgctaaacttagtaaaacttctcgtactgattcatctttcataatggatgggttctctggctccattgatgattctctggattttcagaaaaaaatcctttctcataggtttgatgaaagcatcaa
taccaaattggcaacatgtggaaaaaatgccaatggctttacactagcagAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACTTGTG
AGGTCTTTAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTATACCA
CTTAATAAGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAATATA
GATTTTCTTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCGGATATCT
GTTCTAGGCTTATTATGGTTCTGCCAGATAACACATGAAGGGTGAGCAAGTGAATACAAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGCAGCAGAC
AGGAAGGAGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGATGGCTTC
TATTCCAGAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTAAGATAGT
CATGAGAAAGTTTCCCTAACTCCAATTTTTTCTTCCACA

Intron 5 GTGAGCAAGT ... TGATTAGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	88.24	3	20	25
A2	72.97	5	6	21
A3	74.07	7	16	24
A4	55.56	8	8	12
A5	100	0	1	2
A6	67.66	27	37	76
A7	65.49	39	67	81
A8	69.78	42	76	118
A9	67.96	33	68	72
A10	54.55	25	20	40

>TRINITY_DN46312_c0_g1_i8 from sample A7 / Example spliced isoform

CGTACATCAAACACATTAGAACAAATTTCATCTCCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGATGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTAGAGCAGGTT
TGGTTGATGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATGAAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGATAGATGG
GCTGACATGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAGATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCCCTGGAAT
CCGGCATACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAAACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTTGTTCTGG
GTCCATTTATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTA
ATGGCTCTAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTT
CAACCCAAAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAATTATGCACTGGTTCAATTTGCAGGGCACCACATATTCAAATAAAC
CTCTTTTCACTCATCAAGAATGGATTGCAAATAACCTGTGCAACTTTGCTGAGAGCTTTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCATGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCCTTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACTCATTCAG
GTGGTTCAGAATCATGCATTTGAAATTTCAAAACGTGTGTATAACTCAAGCTGCATGCCTGATAAGTTGCTACTTCTCATTTTAAGTCTACTGAAAGAATGTCAACCTCGAAAGCAATTTTCCAATAATATGAAAGGTTGCACAATGAAACATGAGAGAAAACAAGCATTAGTAGAGTTTGATGGAAAGGAGGATTTACC
GGGATACTGTACACTTGTCACAAATATTTCTGATGTTATCCTTTCTATAATGGGGGAACTTATTTCATATGCAAGGTCAACATTCACAATATTTTGGTCTGCTGATTTCTCATGGGATGGGCCATTACCTGGTTCAGTAACTGGAAAACTTGGTGGACCAAGTCAACGGCGACTTCCATCTTCTGCAACTTCAGTAGTCC
TGCAAGCAATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAA
GCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGTGGTGTTGCTTGGATTC
TTTCTTGTCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAGCGAGTGC
CTTCTGATGGTAGTCTTCACAACCAAAAGAAAGTTGAGATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCCCTGAAG
TGGTTCCTTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATGTAGC
AGCCAGAGAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATATGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAAATGTTTC
TTTTGGAGCTTATAGATTCTGTGGTCAATGATGTGGACCTTGCCAGGGAACTGTACAAAAAGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCATAAATGCCTTCATATGAACAACTTGCCTGCAGTT
CGCCAGTATATTGAAATCTTTGCTATGCAATTATACTTAAAGTTTCCATCCATGATAGTGAAGCAAATGACTCCAATATTGTATGATTACAGTATGAAGCCACAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCTCCAGTTTGAGCTCCTGGAGGAGTTGCTTCCTCC
ATTGCTTCCATTTTTGACTTCACATCACCACAGTTTGCGTGGCTTCTCTCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGGTTGAGAT
CTTCAGTGGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGATGCT
GTAACTCTTAAGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCATCAA
TACCAAATTGGCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACTTGTG
AGGTCTTTAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTATACCA
CTTAATAAGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAATATA
GATTTTCTTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCGGATATCTGTTC
TAGGCTTATTATGGTTCTGCCAGATAACACATGAAGGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGCAGCAGACAGGAAGGAGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAAC
ATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGATGGCTTCTATTCCAGAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGA
ATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTAAGATAGTCATGAGAAAGTTTCCCTAACTCCAATTTTTTCTTCCACA

>TRINITY_DN46312_c0_g1_i3 from sample A7 / Example unspliced isoform:

TCAGGTAGTACTTTGGTAATGTTGATGTTGAGGTTTGTATTGCATTAGAGAAGGTATGATCTTGGTGCTTTGGAAAGAAGTTTCGGGTTCTCATATATATTGTCCTTGAATGATGCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGG
AGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGGTTGAGATCTTCAGTGGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTA
GAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGATGCTGTAACTCTTAAGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGG
CTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCATCAATACCAAATTGGCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAG
ATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACTTGTGAGGTCTTTAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTC
TTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTATACCACTTAATAAGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAA
TGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAATATAGATTTTCTTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTT
CCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCGGATATCTGTTCTAGGCTTATTATGGTTCTGCCAGATAACACATGAAGGgtgagcaagtgaatacaaattacaatgcaagaacatatttgtttagcaagataaaccggccaagttaccaacaacattaaaatgtgcaagctt
gatatgattagtagGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGCAGCAGACAGGAAGGAGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCAT
TATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGATGGCTTCTATTCCAGAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTT
AGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTAAGATAGTCATGAGAAAGTTTCCCTAACTCCAATTTTTTCTTCCACA

Intron 6 GTATGCTGAT ... TTCTGAACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	48.48	17	0	16
A2	43.33	17	1	13
A3	45.83	13	2	11
A4	44.44	10	1	8
A5	43.48	13	0	10
A6	33.33	2	0	1
A7	33.33	2	1	1
A8	25	3	0	1
A9	30	7	0	3
A10	46.67	8	0	7

>TRINITY_DN116618_c3_g1_i28 from sample A3 / Example spliced isoform

TATGGGAATTTTCTTGGAATGTTCTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTG
GTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGT
TACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCA
ACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGTGGTGTTGCTTGGATTCTTTCTTGTCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAA
AGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAGCGAGTGCCTTCTGATGGTAGTCTTCACAACCAAAAGAAAGTTGAGATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTT
GTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCTCTGAAGTGGTTCCTTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGG
AATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATGTAGCAGCCAGAGAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATATGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAG
GTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAAATGTTTCTTTTGGAGCTTATAGATTCTGTGGTAAATACACTCATTGGCATTTTGATTTTTTCTAACCTTAAACATTGAGTAATTGTATGTTGTAAGAGATAAATTTCTGTTTCAGTGAGCCCTCTGAA
CTTCAATAAAATCTAAACTATAGCTACAAGAGATGGTGCAGCCAGAGGCATGTTCAAAGCTGATTAGACATAAAGCAAACACTCTTAAAGATTAAAATTGCTATGAATTTCTTTTTAACTGATTCAGGATAAGTAATTGCACTTTCTCTATTTCTGTGAGACCAAAGGTTCCATTCTTAAAAATTAGATACTATGACTTT
AGTTTTTTTTATATGTTTAATGAATGGATTTAACTATTTTAGATATCTTATCAGCACTAGATTGATATTAAATGGGACGGTGTAACAGCTACACCACAGCCAGACTTTGACTGTGGGTTGGCATTTTACATGGTATAACTCAGGGTTGTGTATGTTGGG

>TRINITY_DN116618_c3_g1_i9 from sample A3 / Example unspliced isoform:

CTGCGTCAATACCTCAGGATGAGgtatgctgatgttttgaaaagacaatgagttgcatataaaatatgcctttgctctactggaatttcactagaaattttttttattgtttaacaagggttttagaagcatcttaactaatttcttactcgctgtttacttacttggtctccctttctctggaaactaattttctcatc
agaagtttgtacatgaatatttgccatgctgataaaacatttttttcattaagcttgtcctataatcatgctaacttttagtatgtaagtgctatgttgttttctgaacagATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTAC
TTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGA
GGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTT
GAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGTGGTGTTGCTTGGATTCTTTCTTGTCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGA
TAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAGCGAGTGCCTTCTGATGGTAGTCTTCACAACCAAAAGAAAGTTGAGATTATGTGGTCATTGGTGCAAT
CTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCTCTGAAGTGGTTCCTTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCA
GCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATGTAGCAGCCAGAGAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATATGT
AAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAAATGTTTCTTTTGGAGCTTATAGATTCTGTGGTCAATGATGTGGACCTTGCCAGGGAACTGTACAAAA
AGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCATAAATGCCTTCATATGAACAACTTGCCTGCAGTTCGCCAGTATATTGAAATCTTTGCTATGCAATTATACTTAAAGTTTCCATCCATGGTAAGT
CATGTTTCAGTTATAATGCTAGCATATAAGGACTTGGCTTTAGCTTATAAATCTGTTTGGATCACATTTTAAATTGGATATTATTTGATATTAGTTTTTGATAAGAAGTGTCTAACCTTTGATTTCTG

Intron 7 GTGTGTAGTT ... TGCTGTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	12.68	31	6	3
A2	15.79	24	3	6
A3	15.62	27	4	6
A4	13.79	25	7	1
A5	0	3	0	0
A6	11.11	12	0	3
A7	18.18	9	3	1
A8	6.67	14	0	2
A9	4	12	0	1
A10	22.58	12	4	3

>TRINITY_DN46312_c0_g1_i4 from sample A7 / Example spliced isoform

CACTTTTCCACCACTTCTGAAGGATCATCTCAAGGAGGATCAACAATTTACTTTGGATGCAAAAGAACATAAATTTCTACTAGCTTTTGTTTCAACAGTTACACATCTATTCAAGAAACCAGAAAGTGATATGGGTGCACTGAAAGCACTTATCTGGATAGTGTATTTCCCAATATTGAAAAGGACTTCCGTTGAAAACT
TTGTTTTGCATAATCAGGTTGCAGAGGCATTGGCTACAATTGCCATTGAAAGACATTCTTGGGGTGACATGGAAGCGACCCTGCTACCGTACTGTTTGACATCAGTGGTATCTTCTGTTGCTTCTGAGCTGCAAGTCCTTTCATCGTCTGATTTGCAAGATGATGCCTACCCATTGAGTTTGGAAATCATAACCTCTTTG
AGATCTTTAGACCTAAATCAGGAACATTTAGAACTCGCAAATAGGTTTTTACCATGCCCTGTAGCATGCCAGCTATTGGCAACATTATTGCTGGCAGCTTTGAAGGTATTGAGTTCAAATGAGGTTGGAATGCCACTGAAGGAGATGTATGAGAGGGTTAACTCGTCTGCAGGGAAATTTGCTAGGCAGATGGTTTCAGA
TCTCTTGGACCCAGCGTTAAACATGCTTTCACAATGTTCAGATTATAAAGTGCGGCAGTGTGCAATGACCGTGCTTTTACCACCTATCTTGCAGACAGTAGATATACTTGCATCATTTGAAGCTTGTTCTTCTGGGCAACTATCTGACAATTCCAGGGTACTTGTCATGCAGAAGGTATGGAGCTGCTTGAAGTGTTTGT
TTTCTCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGATGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTAGAGCAGGTTTGGTTGATGAAGAACATTTGACACGGAAA
AGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATGAAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGATAGATGGGCTGACATGGAGGCAAAGTCCTTAGGTGT
AGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAGATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCCCTGGAATCCGGCATACAGTGATATGGGATCATCAAA
GTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAAACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTTGTTCTGGGTCCATTTATACAAGCACTGAATGATCCA
ATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTAATGGCTCTAGCTTTGTGCATTAAAGAAGC
TGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTTCAACCCAAAGTATAGATCTCAAGTGTGTG
AATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAATTATGCACTGGTTCAATTTGCAGGGCACCACATATTCAAATAAACCTCTTTTCACTCATCAAGAATGGATTGCA
AATAACCTGTGCAACTTTGCTGAGAGCTTTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCATGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCCTTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACTCATTCAGGTGGTTCAGAATCATGCATTTGAAATTTC
AAAACGTGTGTATAACTCAAGCTGCATGCCTGATAAGTTGCTACTTCTCATTTTAAGTCTACTGAAAGAATGTCAACCTCGAAAGCAATTTTCCAATAATATGAAAGGTTGCACAATGAAACATGAGAGAAAACAAGCATTAGTAGAGTTTGATGGAAAGGAGGATTTACCGGGATACTGTACACTTGTCACAAATATTT
CTGATGTTATCCTTTCTATAATGGGGGAACTTATTTCATATGCAAGGTCAACATTCACAATATTTTGGTCTGCTGATTTCTCATGGGATGGGCCATTACCTGGTTCAGTAACTGGAAAACTTGGTGGACCAAGTCAACGGCGACTTCCATCTTCTGCAACTTCAGTAGTCCTGCAAGCAATTTTGGCTCTTAAGACTGTT
GCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGT
ACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGTGGTGTTGCTTGGATTCTTTCTTGTCAATTTCCTGGCGGTCTGTAA
ATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAGCGAGTGCCTTCTGATGGTAGTCTTCACAACCAAAAG
AAAGTTGAGATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCCCTGAAGTGGTTCCTTGAAAGGCTTCTTGAGCAAGG
TGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATGTAGCAGCCAGAGAATACTTAACTCTTGTTCAAA
GCACTGATCCTGAACTAACCGAGGCATATGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAAATGTTTCTTTTGGAGCTTATAGATTCTGTGGTCAAT
GATGTGGACCTTGCCAGGGAACTGTACAAAAAGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCATAAATGCCTTCATATGAACAACTTGCCTGCAGTTCGCCAGTATATTGAAATCTTTGCTATGCA
ATTATACTTAAAGTTTCCATCCATGATAGTGAAGCAAATGACTCCAATATTGTATGATTACAGTATGAAGCCACAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCTCCAGTTTGAGCTCCTGGAGGAGTTGCTTCCTCCATTGCTTCCATTTTTGACTTCACATCACC
ACAGTTTGCGTGGCTTCTCTCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGGTTGAGATCTTCAGTGGAGAAACACTTGGATGTATTT
GATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGATGCTGTAACTCTTAAGAATGAAGAACTTAGAAG
CATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCATCAATACCAAATTGGCAACATGTGGAAAAAATG
CCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACTTGTGAGGTCTTTAAAGCAGCGAGCTTAATTATT
GCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTATACCACTTAATAAGTATTCATTCCCACGAAAAAC
GGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAATATAGATTTTCTTCTAATAGCTTTACCTGAGAG
AATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCGGATATCTGTTCTAGGCTTATTATGGTTCTGCCAGAT
AACACATGAAGGGTGAGCAAGTGAATACAAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGCAGCAGACAGGAAGGAGTTTCCTAATTTAAATTTTAG
TCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGATGGCTTCTATTCCAGAAAGGTAGGTCAAGAGGGATC
CTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTAAGATAGTCATGAGAAAGTTTCCCTAACTCCAATTTT
TTCTTCCACA

>TRINITY_DN46312_c0_g1_i12 from sample A7 / Example unspliced isoform:

GATTAATTGCAAGAAACAATCTATGTAATCAAAGATTCATGTTATAGTTCATTATGTTTTTGTAGGTTGAGATCTTCAGTGGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTgtgtgtagttcactgcaaagtttggttca
ccatagagtataatttttttttggacactcattcgttactgcaaatatcatatagataccaaaggaacattttctgcatgctgtgcagGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGATGCTGTAACTCTTA
AGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCATCAATACCAAATTG
GCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACTTGTGAGGTCTTTAA
AGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTATACCACTTAATAAGT
ATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAATATAGATTTTCTTC
TAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCGGATATCTGTTCTAGGCT
TATTATGGTTCTGCCAGATAACACATGAAGGGTGAGCAAGTGAATACAAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGCAGCAGACAGGAAGGAGT
TTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGATGGCTTCTATTCCAGAA
AGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTAAGATAGTCATGAGAAAG
TTTCCCTAACTCCAATTTTTTCTTCCACA

Intron 8 GTATGTGTTT ... TTGCTCTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	13.79	25	2	4
A2	16	21	0	4
A3	7.41	25	0	2
A4	5	19	0	1
A5	40	6	0	4
A6	25	12	0	4
A7	31.25	11	0	5
A8	21.05	15	0	4
A9	11.76	15	0	2
A10	25	12	0	4

>TRINITY_DN132627_c3_g1_i20 from sample A1 / Example spliced isoform

CTAAACTTTGCGTCTAAAGAGTTTAGCAAGGTTTAAGCTCTGAAATAACATTTAGAAAGCAACTTGCCCATTTTCGTTGAATGCAGCCATGGCCATGGCTACGGCAGATGCATTATTGCAGGCGTTGCACAGCATTCCACTGGGGGCGGTTCCAGGACTTGTTGACGCTCTTCTCCTCTCAGCTGGTCTGCACTCTTCAG
TTCTTCTCAATCACCTCATCTACACTTTTCCACCACTTCTGAAGGATCATCTCAAGGAGGATCAACAATTTACTTTGGATGCAAAAGAACATAAATTTCTACTAGCTTTTGTTTCAACAGTTACACATCTATTCAAGAAACCAGAAAGTGATATGGGTGCACTGAAAGCACTTATCTGGATAGTGTATTTCCCAATATTG
AAAAGGACTTCCGTTGAAAACTTTGTTTTGCATAATCAGGTTGCAGAGGCATTGGCTACAATTGCCATTGAAAGACATTCTTGGGGTGACATGGAAGCGACCCTGCTACCGTACTGTTTGACATCAGTGGTATCTTCTGTTGCTTCTGAGCTGCAAGTCCTTTCATCGTCTGATTTGCAAGATGATGCCTACCCATTGAG
TTTGGAAATCATAACCTCTTTGAGATCTTTAGACCTAAATCAGGAACATTTAGAACTCGCAAATAGGTTTTTACCATGCCCTGTAGCATGCCAGCTATTGGCAACATTATTGCTGGCAGCTTTGAAGGTATTGAGTTCAAATGAGGTTGGAATGCCACTGAAGGAGATGTATGAGAGGGTTAACTCGTCTGCAGGGAAAT
TTGCTAGGCAGATGGTTTCAGATCTCTTGGACCCAGCGTTAAACATGCTTTCACAATGTTCAGATTATAAAGTGCGGCAGTGTGCAATGACCGTGCTTTTACCACCTATCTTGCAGACAGTAGATATACTTGCATCATTTGAAGCTTGTTCTTCTGGGCAACTATCTGACAATTCCAGGGTACTTGTCATGCAGAAGGTA
TGGAGCTGCTTGAAGTGTTTGTTTTCTCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGATGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTAGAGCAGGTTTGGTTGA
TGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATGAAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGATAGATGGGCTGACA
TGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAGATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCCCTGGAATCCGGCAT
ACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAAACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTTGTTCTGGGTCCATT
TATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTAATGGCTC
TAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTTCAACCCA
AAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAATTATGCACTGGTTCAATTTGCAGGGCACCACATATTCAAATAAACCTCTTTT
CACTCATCAAGAATGGATTGCAAATAACCTGTGCAACTTTGCTGAGAGCTTTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCATGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCCTTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACTCATTCAGGTGGTTC
AGAATCATGCATTTGAAATTTCAAAACGTGTGTATAACTCAAGCTGCATGCCTGATAAGTTGCTACTTCTCATTTTAAGTCTACTGAAAGAATGTCAACCTCGAAAGCAATTTTCCAATAATATGAAAGGTTGCACAATGAAACATGAGAGAAAACAAGCATTAGTAGAGTTTGATGGAAAGGAGGATTTACCGGGATAC
TGTACACTTGTCACAAATATTTCTGATGTTATCCTTTCTATAATGGGGGAACTTATTTCATATGCAAGGTCAACATTCACAATATTTTGGTCTGCTGATTTCTCATGGGATGGGCCATTACCTGGTTCAGTAACTGGAAAACTTGGTGGACCAAGTCAACGGCGACTTCCATCTTCTGCAACTTCAGTAGTCCTGCAAGC
AATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAATGTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGG
CTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGTGGTGTTGCTTGGATTCTTTCTTG
TCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGATGCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAGCGAGTGCCTTCTGA
TGGTAGTCTTCACAACCAAAAGAAAGTTGAGATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGCACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCTCTGAAGTGGTTCC
TTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAATCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATGTAGCAGCCAGA
GAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGGCATATGTAAATTCAGAACTTTATGCTCGTGTTACAGTAGCTGTTCTTTTTCACAAGCTTGCTGACCAGGTTGAAAGGGATCAACTATTAGCAAACAAAAGCACATACAAGGATGTCCTGCCTGCATTTAGTTCTGGGAAAATGTTTCTTTTGGA
GCTTATAGATTCTGTGGTCAATGATGTGGACCTTGCCAGGGAACTGTACAAAAAGTCAAGTGCTATTCACCGGCGAAAGACTCGTGTTTGGCAAATGATCTGCATTTTATCACGGTTTGTGGATGAAAGTTCACTTCAGGAAGTTACGCTTGCCATGCATAAATGCCTTCATATGAACAACTTGCCTGCAGTTCGCCAGT
ATATTGAAATCTTTGCTATGCAATTATACTTAAAGTTTCCATCCATGATAGTGAAGCAAATGACTCCAATATTGTATGATTACAGTATGAAGCCACAGGCACTTTCTTCCTATGTCTTCATCGCAGTCCATGTATTGATGAATATTTCCCCAATTTCTCTCCAGTTTGAGCTCCTGGAGGAGTTGCTTCCTCCATTGCTT
CCATTTTTGACTTCACATCACCACAGTTTGCGTGGCTTCTCTCAGATTTTAGTGTATCGAGTACTCCGTAAATTCTTGAATATCACACAATCTCCTATGCAAATGGAACACCAAAATATTTCTTTGGAGAAGAAGTGCTTACAATCTCTTATTGCATATTTGGAGGGAAATGCTGATTGTACAAGGTTGAGATCTTCAGT
GGAGAAACACTTGGATGTATTTGATCCTGTTGCTTCAGCAACACCACGGGGACTATTCTGTTTCAAAAATGGCGATACTGACCCATCTACTGAGCTCCCTTTTGAGCGCGTTCCAGTTTCTATTGTAGAACATGTGATAGACTTTCTCAATGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGATGCTGTAACTC
TTAAGAATGAAGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCATCAATACCAAA
TTGGCAACATGTGGAAAAAATGCCAATGGCTTTACACTAGCAGAAATTGAGGTTGAAGATCAATTGCTGATGTCAACGATAGAGTCACGAATAAAAGAAATGGACAAAATGACAGGGGGACGACAAGATTTGATCGTTGTTGCCTCTTTGCTAGGACGCATTCCTAATCTTGCAGGATTGGCACGAACTTGTGAGGTCTT
TAAAGCAGCGAGCTTAATTATTGCTGATGCAAGTATAATACAAGATAAACAGTTCCAGTTAATCAGCGTCACGGCAGAGAAGTGGATTCCAATACAAGAAGTACCTGAATTGAACCTTAAAGAATTCTTGAAGGCAAAGAAGAGGGAAGGGTACTCAATTTTGGGATTGGAGCAGACAGCAAACAGTATACCACTTAATA
AGTATTCATTCCCACGAAAAACGGTCTTCGTACTTGGAAGAGAGAAAGAGGGAATTCCTGTTGATATCATCCATGTACTGGATGCATGTGTGGAAATTCCTCAATATGGTGTTGTCAGATCTCTAAATGTTCATGTCAGTGGTGCTATTGCAATATGGGAATATACTCGGCAGCATCATCAGGAGTAAATATAGATTTTC
TTCTAATAGCTTTACCTGAGAGAATCATAGGGCGAGAAACAAGGCATGAAAAAATGGATTTATTCTTTCAGAGATTCATTATCACCCTTATGACAAGGCAGTTAAGATGATCTGCAGACTTGATTTTCCATCAACCAATTATGATGTTTTCTTTGCAAGCTCTCTGTTGGAGGACAAGGGCAATCGGATATCTGTTCTAG
GCTTATTATGGTTCTGCCAGATAACACATGAAGGGTGAGCAAGTGAATACAAATTACAATGCAAGAACATATTTGTTTAGCAAGATAAACCGGCCAAGTTACCAACAACATTAAAATGTGCAAGCTTGATATGATTAGTAGGGATGAAAGTGCATGCAGAGGAGCAGTGCTGAAGCAATTGCTGGCAGCAGACAGGAAGG
AGTTTCCTAATTTAAATTTTAGTCGATATATCAACTTGATACCAGATATTAGTTGAAAACTCCGAGTTTTGTGGAAAACTCCTGCCTGCAAGTTTCTGCTAAACATTAAACAGTACACCTGGAGCATTATTGAGTAGAAAATTGGCAAGGGTACCCTGAACAGAAATATGTGTGTGGATACCCTGATGGCTTCTATTCCA
GAAAGGTAGGTCAAGAGGGATCCTCTGTTGATTTGAATCTTTTGTTTTAGGTTGTTTCTTCTTTATTCAAAGGAGGTTGTTGTTCATAAAGTAGTACATTATGAATTTATGGTATAAGAGTCATTTTAGAAGATCTAGTTCTCTCCTTGGACATTCCCGAGGAATATTCTTATGACAGATTTTGTAAGATAGTCATGAGA
AAGTTTCCCTAACTC

>TRINITY_DN132627_c3_g1_i8 from sample A1 / Example unspliced isoform:

ACATGTGATAGACTTTCTCAATgtatgtgttttcctttttgtaattgaatatagatacgtcctatgtggtgctacctttttcgcatgacgtatgtggttacattatttatcaaaaatatgatgtgtatatcttgctctcagGGGGTCAGAGGGGAGCTGCGGGTTGCCATGGAAGAAGATGCTGTAACTCTTAAGAATGA
AGAACTTAGAAGCATGACCAACCATGACAATCTATATTCAGACATGCAGGAAGGAAATGCTAAACTTAGTAAAACTTCTCGTACTGATTCATCTTTCATAATGGATGGGTTCTCTGGCTCCATTGATGATTCTCTGGATTTTCAGAAAAAAATCCTTTCTCATAGGTTTGATGAAAGCATCAATACCAAATTGGCAACAT
GTGGAAAAAATGCCAATGGCTTTACACTAGCAG

Intron 9 GTTTGTGCCC ... GTGGATGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	33.33	17	11	6
A2	22.22	21	7	5
A3	20	24	3	9
A4	27.45	37	24	4
A5	14.89	20	3	4
A6	20	2	0	1
A7	23.81	8	1	4
A8	-1	0	0	0
A9	23.81	8	5	0
A10	17.24	12	5	0

>TRINITY_DN132627_c3_g1_i14 from sample A1 / Example spliced isoform

TAACTAATTTCTTACTCGCTGTTTACTTACTTGGTCTCCCTTTCTCTGGAAACTAATTTTCTCATCAGAAGATTGTACATGAATATTTGCCATGCTGATAAAACATTTTTTTCATTAAGCTTGTCCTATAATCATGCTAACTTTTAGTATGTAAGTGCTATGTTGTTTTCTGAACAGATGGGAGCTGAAATCCGAGTTGG
TGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAGTATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTT
TACTACACTATAAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTAATGGCTCTAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACC
TGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTTCAACCCAAAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTA
GGGAGTTTATTGTCAGTGGTGGAGGCTTGCATTCCAAAATTATGCACTGGTTCAATTTGCAGGGCACCACATATTCAAATAAACCTCTTTTCACTCATCAAGAATGGATTGCAAATAACCTGTGCAACTTTGCTGAGAGCTTTCTGAAACCTCAGAAATTTTATCCCTCTGTTTCTTATGATGATGAAGAATTGGATGCA
TGGCGTGTTGAAGCAGACAGGTGGGCAAGATTATTTTGCCTTGGAGTATTAGAAGAGCATCAGTTCTCACAAATACTCATTCAGGTGGTTCAGAATCATGCATTTGAAATTTCAAAACGTGTGTATAACTCAAGCTGCATGCCTGATAAGTTGCTACTTCTCATTTTAAGTCTACTGAAAGAATGTCAACCTCGAAAGCA
ATTTTCCAATAATATGAAAGGTTGCACAATGAAACATGAGAGAAAACAAGCATTAGTAGAGTTTGATGGAAAGGAGGATTTACCGGGATACTGTACACTTGTCACAAATATTTCTGATGTTATCCTTTCTATAATGGGGGAACTTATTTCATATGCAAGGTCAACATTCACAATATTTTGGTCTGCTGATTTCTCATGGG
ATGGGCCATTACCTGGTTCAGTAACTGGAAAACTTGGTGGACCAAGTCAACGGCGACTTCCATCTTCTGCAACTTCAGTAGTCCTGCAAGCAATTTTGGCTCTTAAGACTGTTGCTGAGTGGACAATATGGTGTGCATATTTGAGGGATACCATGGTTCCTGATTCTGTGATCATATTATTATGGGAATTTTCTTGGAAT
GTTGTTACTGCGTCAATACCTCAGGATGAGATGGGAGCTGAAATCCGAGTTGGTGCATATGAAGCTTTGGTCTCGGTTTGTGAAGCATTGGCTGTCACAACTCGTCCCTCGGTACTTACTTCCATGAAGGCTGTATTAAGTTTTGAGGACACACCAGAGGAAAGGCTGATAGATGAATTGGTTTGGAGGTTTCTCCAAAG
TATCAACGTTTTTCTTCAAACAGGGTCATTGGCAAGAAGTCGTCGAGCAATTTTACTACACTATAAGGTAATTTCTTGTTCCTTGCTTTCACTAATATCAATTTTGTTGAACCTTTTTTTTTGTTTCCAAGGAAAAGATGTATATTTATTATTTCAGTCAGAATCATGAAGTATACTAAGATGTGTGCTTGTAAGTGCTC
AAAATTGCTCTTTGAAGAGATCGTCCAGCAAAAATCATAAAATGTTTCTTCACAATTTCCTTGTAGTAGTCTTGATTATATGGTGTTGCTTGGATTCTTTCTTGTCAATTTCCTGGCGGTCTGTAAATACTTGTCCAGGAATGCTGGACCATGATGATAGTGCGGTTTCTGATGCAATTTTGGAGAATGTTGTTTTTGAT
GCAATTGACAGTTTGGAAAGTGCGAATGAGGACTCCATTCTTCCCATTTTGAGATCTGTAAGATGGGTGATGAATTGGGGTTTGTTAAAGCGAGTGCCTTCTGATGGTAGTCTTCACAACCAAAAGAAAGTTGAGATTATGTGGTCATTGGTGCAATCTGCTTGGACAGCCTGTTCCGATTGCAATAAGCGAAGGGTTGC
ACCTATAGCTGCACTTTTGTCAGCTATCTTTCATCCATCTATTTTCAGTGATATCTATATGCATGATGGTGGAAGTAATAGACCAGGACCTCTGAAGTGGTTCCTTGAAAGGCTTCTTGAGCAAGGTGTTCGAAGTCCTCGAACTATGCGTCTCTCAGCTCTGCACTTAACTGGAATGTGGCTTTTATATCCTGCAACAA
TCACGTTTTATATAAAGGAATTGAAGCTTCTTACTCTTCATGGCAGTGTGGCTATTGATGAGGATCTGGATGGGGAGTTGCTTGAAAACTATGTAGCAGCCAGAGAATACTTAACTCTTGTTCAAAGCACTGATCCTGAACTAACCGAGG

>TRINITY_DN132627_c3_g1_i13 from sample A1 / Example unspliced isoform:

GTAGATAATTTGGTGGCTATGATATCTGCAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGAGTTGGGCTAATGGCTCTAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACA
GACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAAACAACACTTCAACCCAAAGTATAGATCTCAAGgtttgtgcccaaccaggaaaatatgatatcctttggtcctttttcctatttgccttttatggtgccaggattaaag
actttgctacattaacttcaataatggcactccattaatatttggattttatggattctagagccatctataatattcctaactatttgattgtggatgcagTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAG
TTTATTGTCAGTGGTGGTGAGTATAACAATTTGATGTGGTGATTTTTTTTTAAACTTTCAGGATAAAACTGGACTATAGTATGTTGACTTTTTTCTGCA

Intron 10 GTAATCTCAT ... TTGTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	32.64	23.2	7.8	6
A2	30.36	15.4	4.2	6
A3	33.27	24.6	10.4	7
A4	25.88	23	9.4	3
A5	29.47	12.6	4.2	4
A6	31.43	2.6	2.2	0
A7	33.33	4	2	2
A8	13.33	2	2	0
A9	13.33	2	0.8	0
A10	23.92	5.4	3	0

>TRINITY_DN116618_c3_g1_i20 from sample A3 / Example spliced isoform

ACCAGAGCAGGACTAAACTTTGCGTCTAAAGAGTTTAGCAAGGTTTAAGCTCTGAAATAACATTTAGAAAGCAACTTGCCCATTTTCGTTGAATGCAGCCATGGCCATGGCTACGGCAGATGCATTATTGCAGGCGTTGCACAGCATTCCACTGGGGGCGGTTCCAGGACTTGTTGACGCTCTTCTCCTCTCAGCTGGTC
TGCACTCTTCAGTTCTTCTCAATCACCTCATCTACACTTTTCCACCACTTCTGAAGGATCATCTCAAGGAGGATCAACAATTTACTTTGGATGCAAAAGAACATAAATTTCTACTAGCTTTTGTTTCAACAGTTACACATCTATTCAAGAAACCAGAAAGTGATATGGGTGCACTGAAAGCACTTATCTGGATAGTGTAT
TTCCCAATATTGAAAAGGACTTCCGTTGAAAACTTTGTTTTGCATAATCAGGTTGCAGAGGCATTGGCTACAATTGCCATTGAAAGACATTCTTGGGGTGACATGGAAGCGACCCTGCTACCGTACTGTTTGACATCAGTGGTATCTTCTGTTGCTTCTGAGCTGCAAGTCCTTTCATCGTCTGATTTGCAAGATGATGC
CTACCCATTGAGTTTGGAAATCATAACCTCTTTGAGATCTTTAGACCTAAATCAGGAACATTTAGAACTCGCAAATAGGTTTTTACCATGCCCTGTAGCATGCCAGCTATTGGCAACATTATTGCTGGCAGCTTTGAAGGTATTGAGTTCAAATGAGGTTGGAATGCCACTGAAGGAGATGTATGAGAGGGTTAACTCGT
CTGCAGGGAAATTTGCTAGGCAGATGGTTTCAGATCTCTTGGACCCAGCGTTAAACATGCTTTCACAATGTTCAGATTATAAAGTGCGGCAGTGTGCAATGACCGTGCTTTTACCACCTATCTTGCAGACAGTAGATATACTTGCATCATTTGAAGCTTGTTCTTCTGGGCAACTATCTGACAATTCCAGGGTACTTGTC
ATGCAGAAGGTATGGAGCTGCTTGAAGTGTTTGTTTTCTCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGATGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTAGAGC
AGGTTTGGTTGATGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATGAAAGGGAAGTGGCTATTCATCATAAGACAAAGAGGGATA
GATGGGCTGACATGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAGATATCTTTATTATTGCCCACTGTAGAGGGTTGGAGCCCT
GGAATCCGGCATACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAAACTTGGAAACATTGGAGAACTTGTTCCACAGTGGTTTGT
TCTGGGTCCATTTATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGGTATTTTTGATATTATGTATGTGATTTGATTAATTGTTTCATGTCCCAAAAAGTGTGTAAATTAG
GAGCTAAGCTCCTTTAAAAAGAGGATACAGAAAATCATATTCAGGTGCAGATTGTTTTTGAGTGGTGAACATGATCTCCAGTATCCCAGACTAGCAACAGGTTATTGGTGTTCAGTAAAGTTGAAAAAAGGAGAGATTCAGGCACTCTTTAGAAAGATCAATCAATGCAATTTTTCATA

>TRINITY_DN116618_c3_g1_i7 from sample A3 / Example unspliced isoform:

ACCAGAGCAGGACTAAACTTTGCGTCTAAAGAGTTTAGCAAGGTTTAAGCTCTGAAATAACATTTAGAAAGCAACTTGCCCATTTTCGTTGAATGCAGCCATGGCCATGGCTACGGCAGATGCATTATTGCAGGCGTTGCACAGCATTCCACTGGGGGCGGTTCCAGGACTTGTTGACGCTCTTCTCCTCTCAGCTGGTC
TGCACTCTTCAGTTCTTCTCAATCACCTCATCTACACTTTTCCACCACTTCTGAAGGATCATCTCAAGGAGGATCAACAATTTACTTTGGATGCAAAAGAACATAAATTTCTACTAGCTTTTGTTTCAACAGTTACACATCTATTCAAGAAACCAGAAAGTGATATGGGTGCACTGAAAGCACTTATCTGGATAGTGTAT
TTCCCAATATTGAAAAGGACTTCCGTTGAAAACTTTGTTTTGCATAATCAGGTTGCAGAGGCATTGGCTACAATTGCCATTGAAAGACATTCTTGGGGTGACATGGAAGCGACCCTGCTACCGTACTGTTTGACATCAGTGGTATCTTCTGTTGCTTCTGAGCTGCAAGTCCTTTCATCGTCTGATTTGCAAGATGATGC
CTACCCATTGAGTTTGGAAATCATAACCTCTTTGAGATCTTTAGACCTAAATCAGGAACATTTAGAACTCGCAAATAGGTTTTTACCATGCCCTGTAGCATGCCAGCTATTGGCAACATTATTGCTGGCAGCTTTGAAGGTATTGAGTTCAAATGAGGTTGGAATGCCACTGAAGGAGATGTATGAGAGGGTTAACTCGT
CTGCAGGGAAATTTGCTAGGCAGATGGTTTCAGATCTCTTGGACCCAGCGTTAAACATGCTTTCACAATGTTCAGATTATAAAGTGCGGCAGTGTGCAATGACCGTGCTTTTACCACCTATCTTGCAGACAGTAGATATACTTGCATCATTTGAAGCTTGTTCTTCTGGGCAACTATCTGACAATTCCAGgtaatctcat
tgcacatgattgccgtgttgttggattattgttctagaaaactgaactaatgttcagtgaacaaaattctctagcaaattgtaagtcatccctgcataaaattttggactctattattctttctctttaattttctgtgtaggctttagaaaaacccttgcaaattagaaagagatccgaaacattgtttgcagGGTACT

TGTCATGCAGAAGGTATGGAGCTGCTTGAAGTGTTTGTTTTCTCAGGGATCGCTTCAGCGCCAAGATGCATACACAGCTTTGTCTTTGTTTGTGGAATTCATGTTGTCATCTTTTCATGATAAACTTGGATTTTCTGGAGATGAAATTTGTTCTAATGTGTTTGATGTACGGTCAGAAAAAGAATTTTGGGAAGAACTTA
GAGCAGGTTTGGTTGATGAAGAACATTTGACACGGAAAAGAGCATTACATGTTCTGAAGGTCACTTTAGAAAAGATGCCACTATCATTAAGCAATGATGATTGTCATAAAAGAGATGATGGATCGAAGGACAAGAATATGCAAGCAAATGGTGATAAGAAGAATGAAAGGGAAGTGGCTATTCATCATAAGACAAAGAGG
GATAGATGGGCTGACATGGAGGCAAAGTCCTTAGGTGTAGGGGTGGTCAATAAAGGACATGATAAGGTCCCTGACTGTTGGCAACGCTGGGAGGCTTTCATTCTTTTGTATGAAATGCTTGAAGAGTATGGTACTCACTTGGTTGAAGCCGCTTGGTCACACCAGATATCTTTATTATTGCCCACTGTAGAGGGTTGGAG
CCCTGGAATCCGGCATACAGTGATATGGGATCATCAAAGTGAGATTGAACATGTGGATGTAGCATTCTTATGGATGACCGTGCTATGGCAGCGCGGATTTGACCATGGAAATCCACAAGTTCGTCGATTGATTATGCAGTCATTTTTGGAGTTGGATTGGACGAAACTTGGAAACATTGGAGAACTTGTTCCACAGTGGT
TTGTTCTGGGTCCATTTATACAAGCACTGAATGATCCAATACACCATAAAGATTTTGGTATTAGAGGCATCTATTCTTCAGAGACAATCAAAGGTGCGGCCAAGTTCATTCGTCAATACTCTGCTTCACTTTCTAGAAGTGCTCGTGAAACGTTTGTTCAGCATTTGGCATCTTTTGTGAAATCACAGTCTCTTGGGCGA
GTTGGGCTAATGGCTCTAGCTTTGTGCATTAAAGAAGCTGCCTGTGGAGATGATTGGATTGAAGATAACGGAACTTTAAAGACGTCTACTCCGTTATCTAAAACAACAGACTGCAATGACATACCTGGCAGGCATACTCTACAAGAAAATACAATTGCCGACTTGGTTGAGGTTCTTCGACTTGTTGTTGAGAACAGTAA
ACAACACTTCAACCCAAAGTATAGATCTCAAGTGTGTGAATATATTATAGTAGCTGCCTCGGCTCTAGTGGTGGTATATGAAGTGCCATTCGACAAGTTTTTACACTTTTTGTCATCATTTCCTAGGGAGTTTATTGTCAGTGGTGGTGAGTATAACAATTTGATGTGGTGATTTTTTTTTAAACTTTCAGGATAAAACT
GGACTATAGTATGTTGACTTTTTTCTGCA