NA ----> NA

Intron 1 GTAAGTTGCT ... TTCTCTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	48.21	29	4	27
A2	45.68	44	0	37
A3	45.57	43	4	36
A4	71.15	15	1	37
A5	85.71	2	0	12
A6	33.93	37	0	19
A7	32.79	82	3	40
A8	26.32	14	0	5
A9	28.46	93	3	37
A10	31.43	72	2	33

>TRINITY_DN112324_c0_g1_i4 from sample A1 / Example spliced isoform

CCCGGAAGAATTTGTCCCGGTCCGCGTGCATAATTTTCTACAAAATCTGTATAAATAGGACTTGGTCGCCAAAGACTGCCGGACTGCCAGCGGCCGTTTAACGGACTATTTGTGAGTGTATCGTTATTCTTGCTACGGCTTCGGATTCTGCGAATCGCGGCGAAAACGTAAATCAATATGGAAAACAAGGATTTCAAGGA
GGAGCGATCTCAGGCAAATGATTCAGTTCCCGACGAGAAATTGACTTCTGAGAAACATGTTGATATTGAAGATCATAAAAATAATGTCGAACAAAAGAGTTCAGATATTGAAAAAGAGAGCACTGATGTAGAGAAGAATGAAGCTGATAAGGAGGATGGAGCCACGGTCGATCGAACCTTATACGTATGCGATGTTCCAG
GCGAAGAAAAAGAAACTGAGCCTGTTTTCTACGGAACTGAAAATCCTGAAGCCGAAATTGGACGATCTCCAGAATCCGATTTCGGTTTAAGGGGGGCTGCTTGGCCGGAAAAGGCAACGGCTATAAAGAACTTCTTCATGGAGCGCGGCGTCATGATCCGGAAGTTTTCCGAGAAAAGTGGTATTCCCGAAGTTATCCGG
CGTCTTTCCCTGACTAAGAGAGACGAAGCCGATCTAAACGCAGTAGACTCTGAGGGTAAAATTGCCACTGAGGAAACCAAAATCTCAGCGGAAGAAGATAAAAAGGAAACTAATGACGGGAAGACTTTTAAGGACTGGGCTGTGTGGAATCCCCTGAATTTGGTTAAGAACAGTTTAGAGAAACAATATAATCAGAGCCA
GGGTGCACACTTACCAGCATTAGTTGTAGAGCCTGCCTTTAAGGGCAGGATCATTTTATTTTCCTGTTCGGAGAGCCAGCCATGCCGAGCAGCTAGATCTTTCTTGAGACAAAAAGGACTCAAATTTGTCGAAATCAACATTGACATTTATCCCGGCAGGAAGACGGAGCTAGAAAACATAGCAGGTTCTTCATCTGTTC
CAAAGATTTTCTTTAATGAATTGTGCTTGGGAGGGATGAATGAAGTTAGGGCCATGGAAGAGTCTGGCGAACTCGATGAAAAGATCAAGGGATTGATTGAAACCGAGCCTCCTTCTTCGGCCCCTTTGCCACCGTCTGCAGGGGAAGATGATTTCGGGAACAATGGGATGGTGGATGAGTTTGCTAATGTTGTCAGAAAA
CTCCGGGAAGCAGTGGTTGTCAAGGATAGGTTTTATAAAATGCGGATGTTCACCAGGTGCTTTGTTGGATCGGAAGCGGTCGATTTCTTGTCAGAGGATCAGTTGCTGGAGAGGGATGAGGCAGTTGAATTTGGACGAAAGCTCGCTTCAAAACATTTTTTCCACCATGGTCTAAATGAGAATGTCTTCGAAGACGGAAA
TCATCCTTATCGTTTCATGGAACATGATCCGGTTGTTTCCGCCAACTGCTATAATTTTACTGGATGTACAAATGACATGAAGCCCAAACCTCCAGCTGAAATTGCAGCTAGACTGAGGAGCCTGACCCAAGCAATTTATGAAGCTTACATCTCTGATGATGGGAAGCATGTAGATTACAGAAGCATTGGTGCCAGTGAAG
AGTTTATAAGGTACTTGAAAGTGATTGAGGAACTTCACAGAATTGATTTACATGACTTATCCAGAGAAGAAAAACTTGCATTCTTCATCAATCTGTATAATATGATGGCAATTCATGCAATTGTGCTGTGGGGTTACCCTGATGGACCTCTGGAGAGGAGAAGATTTTTTGGTGAATTTAAATATGTCATTGGTGGCTAT
TCTTATTCACTTTCAGCCATTCAAAATGGAGTTTTGCGCAGTAACAAAAGACCCCCTTACAATTTGATTAAACCTTTTGGGTTAAAAGACAAACGCATCGAGGTTGCCTTATCAGATCCAGAACCTTTGGTTCATTTTGCCTTGGTGTGTGGTTCAAGATCAAGCCCTGCCATCAGATGCTATTCGCCTGGAAGTATTGA
TGAAGAACTAAGGCTAGCTGGAAGGATATTTTTTGATGATGGTGGTTTCTTGATTGATGTGGAGAACAAGCTTGCTTCAGTTAGCAAGATTATGAATTGGTACAGTGTGGACTTTGGCAAAAACGAAACAGAAGTCATGAAGTTTATTGCAAACTATTTGGAACCCTCCAAGTCAGAACAGCTGTTGGAATTATTGAATG
GTAATCAACTGAAGGTCACATACCACAGTTATGATTGGGCTTTGAATTGCTAAGTCCAATGTTACCTGTCATGCCCTAGATCAATTCATAGTCATCTATCAAATGGGATCTGTATCCCAATTTTATTGGGATGGAAGCTGAATTATTATGAAAGTCTGGAATTTTGCTGATGGTTGTGAGATAGAAGATCAAACGATCTG
TTTACTAAGTTTTGGTGCAAAGTCTTGTGAATAAGTAAGAAACACGGACCATTTTTGTTTTTGAAGTACTGGAAAGTCTGCGGTTCAAGCCCTTCCAAGCTGTTTGGTAAATGTGGCACGCCATTTTATTATGTTACTTCTTCACCGATTTATTAAAATATATTCTATAGCTATCTTGTCATTTGAACTGATCAATTTAT
TGGACTTCAAACTAGTATGTCTTGAAGCTCTTTGGAAAA

>TRINITY_DN112324_c0_g1_i2 from sample A1 / Example unspliced isoform:

CCCGGAAGAATTTGTCCCGGTCCGCGTGCATAATTTTCTACAAAATCTGTATAAATAGGACTTGGTCGCCAAAGACTGCCGGACTGCCAGCGGCCGTTTAACGGACTATTTGTGAGTGTATCGTTATTCTTGCTACGGCTTCGGATTCTGCGAATCGCGGCGAAAACGTgtaagttgctcttaaacatcccgattgcgct
gcgctagtctttatctttactgagttgtcttcttagaaatttttgtttttctatggttcttcatggaaaattttgttcatccttgtggagaattcatttaggttttccttttccggttctgtttcgctgtgttttcagtttaatagcggtgacagtcgttagaatcttccattgcttttggatttaggcattttcaggaa
gaatgactcagtgaggatttattatggtagacagaccattttattagagaagtattgccatttcattgtagatttgcggaaaaaacaatttccgccaagaaaatctagttctgcgttgtgaaattttgactgtctattattcgtttattgttattttctctgtagAAATCAATATGGAAAACAAGGATTTCAAGGAGGAG
CGATCTCAGGCAAATGATTCAGTTCCCGACGAGAAATTGACTTCTGAGAAACATGTTGATATTGAAGATCATAAAAATAATGTCGAACAAAAGAGTTCAGATATTGAAAAAGAGAGCACTGATGTAGAGAAGAATGAAGCTGATAAGGAGGATGGAGCCACGGTCGATCGAACCTTATACGTATGCGATGTTCCAGGCGA
AGAAAAAGAAACTGAGCCTGTTTTCTACGGAACTGAAAATCCTGAAGCCGAAATTGGACGATCTCCAGAATCCGATTTCGGTTTAAGGGGGGCTGCTTGGCCGGAAAAGGCAACGGCTATAAAGAACTTCTTCATGGAGCGCGGCGTCATGATCCGGAAGTTTTCCGAGAAAAGTGGTATTCCCGAAGTTATCCGGCGTC
TTTCCCTGACTAAGAGAGACGAAGCCGATCTAAACGCAGTAGACTCTGAGGGTAAAATTGCCACTGAGGAAACCAAAATCTCAGCGGAAGAAGATAAAAAGGAAACTAATGACGGGAAGACTTTTAAGGACTGGGCTGTGTGGAATCCCCTGAATTTGGTTAAGAACAGTTTAGAGAAACAATATAATCAGAGCCAGGGT
GCACACTTACCAGCATTAGTTGTAGAGCCTGCCTTTAAGGGCAGGATCATTTTATTTTCCTGTTCGGAGAGCCAGCCATGCCGAGCAGCTAGATCTTTCTTGAGACAAAAAGGACTCAAATTTGTCGAAATCAACATTGACATTTATCCCGGCAGGAAGACGGAGCTAGAAAACATAGCAGGTTCTTCATCTGTTCCAAA
GATTTTCTTTAATGAATTGTGCTTGGGAGGGATGAATGAAGTTAGGGCCATGGAAGAGTCTGGCGAACTCGATGAAAAGATCAAGGGATTGATTGAAACCGAGCCTCCTTCTTCGGCCCCTTTGCCACCGTCTGCAGGGGAAGATGATTTCGGGAACAATGGGATGGTGGATGAGTTTGCTAATGTTGTCAGAAAACTCC
GGGAAGCAGTGGTTGTCAAGGATAGGTTTTATAAAATGCGGATGTTCACCAGGTGCTTTGTTGGATCGGAAGCGGTCGATTTCTTGTCAGAGGATCAGTTGCTGGAGAGGGATGAGGCAGTTGAATTTGGACGAAAGCTCGCTTCAAAACATTTTTTCCACCATGGTCTAAATGAGAATGTCTTCGAAGACGGAAATCAT
CCTTATCGTTTCATGGAACATGATCCGGTTGTTTCCGCCAACTGCTATAATTTTACTGGATGTACAAATGACATGAAGCCCAAACCTCCAGCTGAAATTGCAGCTAGACTGAGGAGCCTGACCCAAGCAATTTATGAAGCTTACATCTCTGATGATGGGAAGCATGTAGATTACAGAAGCATTGGTGCCAGTGAAGAGTT
TATAAGGTACTTGAAAGTGATTGAGGAACTTCACAGAATTGATTTACATGACTTATCCAGAGAAGAAAAACTTGCATTCTTCATCAATCTGTATAATATGATGGCAATTCATGCAATTGTGCTGTGGGGTTACCCTGATGGACCTCTGGAGAGGAGAAGATTTTTTGGTGAATTTAAATATGTCATTGGTGGCTATTCTT
ATTCACTTTCAGCCATTCAAAATGGAGTTTTGCGCAGTAACAAAAGACCCCCTTACAATTTGATTAAACCTTTTGGGTTAAAAGACAAACGCATCGAGGTTGCCTTATCAGATCCAGAACCTTTGGTTCATTTTGCCTTGGTGTGTGGTTCAAGATCAAGCCCTGCCATCAGATGCTATTCGCCTGGAAGTATTGATGAA
GAACTAAGGCTAGCTGGAAGGATATTTTTTGATGATGGTGGTTTCTTGATTGATGTGGAGAACAAGCTTGCTTCAGTTAGCAAGATTATGAATTGGTACAGTGTGGACTTTGGCAAAAACGAAACAGAAGTCATGAAGTTTATTGCAAACTATTTGGAACCCTCCAAGTCAGAACAGCTGTTGGAATTATTGAATGGTAA
TCAACTGAAGGTCACATACCACAGTTATGATTGGGCTTTGAATTGCTAAGTCCAATGTTTTTTTTTGACAAGGAATTGCTAAGTCCAATGTTACCTGTCATGCCCTAGATCAATTCATAGTCATCTATCAAATGGGATCTGTATCCCAATTTTATTGGGATGGAAGCTGAATTATTATGAAAGTCTGGAATTTTGCTGAT
GGTTGTGAGATAGAAGATCAAACGATCTGTTTACTAAGTTTTGGTGCAAAGTCTTGTGAATAAGTAAGAAACACGGACCATTTTTGTTTTTGAAGTACTGGAAAGTCTGCGGTTCAAGCCCTTCCAAGCTGTTTGGTAAATGTGGCACGCCATTTTATTATGTTACTTCTTCACCGATTTATTAAAATATATTCTATAGC
TATCTTGTCATTTGAACTGATCAATTTATTGGACTTCAAACTAGTATGTCTTGAAGCTCTTTGGAAAA

Intron 2 GTAGACAGAC ... TTCTCTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	73.68	10	29	27
A2	54	23	17	37
A3	58.18	23	28	36
A4	80.82	7	22	37
A5	93.33	1	16	12
A6	56.86	11	10	19
A7	43.36	32	9	40
A8	50	4	3	5
A9	39.05	32	4	37
A10	50	27	21	33

>TRINITY_DN44358_c0_g2_i2 from sample A9 / Example spliced isoform

ATTTATTTAAAAATAGTTGTTGCGTTGAGGAGGTCCAAGGTTCGCATCCCGCGTAAATCTAAGCGACTGCCATTTACTTTTCCCGCCCGGAAGAATTTGTCCCGGTCCGCGTGCATAATTTTCTACAAAATCTGTATAAATAGGACTTGGTCGCCAAAGACTGCCGGACTGCCAGCGGCCGTTTAACGGACTATTTGTGA
GTGTATCGTTATTCTTGCTACGGCTTCGGATTCTGCGAATCGCGGCGAAAACGTTTTAATAGCGGTGACAGTCGTTAGAATCTTCCATTGCTTTTGGATTTAGGCATTTTCAGGAAGAATGACTCAGTGAGGATTTATTATGAAATCAATATGGAAAACAAGGATTTCAAGGAGGAGCGATCTCAGGCAAATGATTCAGT
TCCCGACGAGAAATTGACTTCTGAGAAACATGTTGATATTGAAGATCATAAAAATAATGTCGAACAAAAGAGTTCAGATATTGAAAAAGAGAGCACTGATGTAGAGAAGAATGAAGCTGATAAGGAGGATGGAGCCACGGTCGATCGAACCTTATACGTATGCGATGTTCCAGGCGAAGAAAAAGAAACTGAGCCTGTTT
TCTACGGAACTGAAAATCCTGAAGCCGAAATTGGACGATCTCCAGAATCCGATTTCGGTTTAAGGGGGGCTGCTTGGCCGGAAAAGGCAACGGCTATAAAGAACTTCTTCATGGAGCGCGGCGTCATGATCCGGAAGTTTTCCGAGAAAAGTGGTATTCCCGAAGTTATCCGGCGTCTTTCCCTGACTAAGAGAGACGAA
GCCGATCTAAACGCAGTAGACTCTGAGGGTAAAATTGCCACTGAGGAAACCAAAATCTCAGCGGAAGAAGATAAAAAGGAAACTAATGACGGGAAGACTTTTAAGGACTGGGCTGTGTGGAATCCCCTGAATTTGGTTAAGAACAGTTTAGAGAAACAATATAATCAGAGCCAGGGTGCACACTTACCAGCATTAGTTGT
AGAGCCTGCCTTTAAGGGCAGGATCATTTTATTTTCCTGTTCGGAGAGCCAGCCATGCCGAGCAGCTAGATCTTTCTTGAGACAAAAAGGACTCAAATTTGTCGAAATCAACATTGACATTTATCCCGGCAGGAAGACGGAGCTAGAAAACATAGCAGGTTCTTCATCTGTTCCAAAGATTTTCTTTAATGAATTGTGCT
TGGGAGGGATGAATGAAGTTAGGGCCATGGAAGAGTCTGGCGAACTCGATGAAAAGATCAAGGGATTGATTGAAACCGAGCCTCCTTCTTCGGCCCCTTTGCCACCGTCTGCAGGGGAAGATGATTTCGGGAACAATGGGATGGTGGATGAGTTTGCTAATGTTGTCAGAAAACTCCGGGAAGCAGTGGTTGTCAAGGAT
AGGTTTTATAAAATGCGGATGTTCACCAGGTGCTTTGTTGGATCGGAAGCGGTCGATTTCTTGTCAGAGGATCAGTTGCTGGAGAGGGATGAGGCAGTTGAATTTGGACGAAAGCTCGCTTCAAAACATTTTTTCCACCATGGTCTAAATGAGAATGTCTTCGAAGACGGAAATCATCCTTATCGTTTCATGGAACATGA
TCCGGTTGTTTCCGCCAACTGCTATAATTTTACTGGATGTACAAATGACATGAAGCCCAAACCTCCAGCTGAAATTGCAGCTAGACTGAGGAGCCTGACCCAAGCAATTTATGAAGCTTACATCTCTGATGATGGGAAGCATGTAGATTACAGAAGCATTGGTGCCAGTGAAGAGTTTATAAGGTACTTGAAAGTGATTG
AGGAACTTCACAGAATTGATTTACATGACTTATCCAGAGAAGAAAAACTTGCATTCTTCATCAATCTGTATAATATGATGGCAATTCATGCAATTGTGCTGTGGGGTTACCCTGATGGACCTCTGGAGAGGAGAAGATTTTTTGGTGAATTTAAATATGTCATTGGTGGCTATTCTTATTCACTTTCAGCCATTCAAAAT
GGAGTTTTGCGCAGTAACAAAAGACCCCCTTACAATTTGATTAAACCTTTTGGGTTAAAAGACAAACGCATCGAGGTTGCCTTATCAGATCCAGAACCTTTGGTTCATTTTGCCTTGGTGTGTGGTTCAAGATCAAGCCCTGCCATCAGATGCTATTCGCCTGGAAGTATTGATGAAGAACTAAGGCTAGCTGGAAGGAT
ATTTTTTGATGATGGTGGTTTCTTGATTGATGTGGAGAACAAGCTTGCTTCAGTTAGCAAGATTATGAATTGGTACAGTGTGGACTTTGGCAAAAACGAAACAGAAGTCATGAAGTTTATTGCAAACTATTTGGAACCCTCCAAGTCAGAACAGCTGTTGGAATTATTGAATGGTAATCAACTGAAGGTCACATACCACA
GTTATGATTGGGCTTTGAATTGCTAAGTCCAATGTTTTTTTTTGACAAGGAATTGCTAAGTCCAATGTTACCTGTCATGCCCTAGATCAATTCATAGTCATCTATCAAATGGGATCTGTATCCCAATTTTATTGGGATGGAAGCTGAATTATTATGAAAGTCTGGAATTTTGCTGATGGTTGTGAGATAGAAGATCAAAC
GATCTGTTTACTAAGTTTTGGTGCAAAGTCTTGTGAATAAGTAAGAAACACGGACCATTTTTGTTTTTGAAGTACTGGAAAGTCTGCGGTTCAAGCCCTTCCAAGCTGTTTGGTAAATGTGGCACGCCATTTTATTATGTTACTTCTTCACCGATTTATTAAAATATATTCTATAGCTATCTTGTCATTTGAACTGATCA
ATTTATTGGACTTCAAACTAGTATGTCTTGAAGCTCTTTGGAAAATGTTAGAAGGAACTTGTTCCTCACATATGCATTTATTTCAATGCTAACTGGGAAACTTGTTTTGCTATATTTGTGAAACTTGATTATGTGAGCCTGGCCTTTTCTGCTAAATTTCACGTGTTCTCTAATTGATCATGCAGTGCATGTTTTGTAAA
ATTTAGGGTTTTTATGTAGAGTTGTG

>TRINITY_DN44358_c0_g2_i1 from sample A9 / Example unspliced isoform:

GTTTTTCTATGGTTCTTCATGGAAAATTTTGTTCATCCTTGTGGAGAATTCATTTAGGTTTTCCTTTTCCGGTTCTGTTTCGCTGTGTTTTCAGTTTAATAGCGGTGACAGTCGTTAGAATCTTCCATTGCTTTTGGATTTAGGCATTTTCAGGAAGAATGACTCAGTGAGGATTTATTATGgtagacagaccattttat
tagagaagtattgccatttcattgtagatttgcggaaaaaacaatttccgccaagaaaatctagttctgcgttgtgaaattttgactgtctattattcgtttattgttattttctctgtagAAATCAATATGGAAAACAAGGATTTCAAGGAGGAGCGATCTCAGGCAAATGATTCAGTTCCCGACGAGAAATTGACTTC
TGAGAAACATGTTGATATTGAAGATCATAAAAATAATGTCGAACAAAAGAGTTCAGATATTGAAAAAGAGAGCACTGATGTAGAGAAGAATGAAGCTGATAAGGAGGATGGAGCCACGGTCGATCGAACCTTATACGTATGCGATGTTCCAGGCGAAGAAAAAGAAACTGAGCCTGTTTTCTACGGAACTGAAAATCCTG
AAGCCGAAATTGGACGATCTCCAGAATCCGATTTCGGTTTAAGGGGGGCTGCTTGGCCGGAAAAGGCAACGGCTATAAAGAACTTCTTCATGGAGCGCGGCGTCATGATCCGGAAGTTTTCCGAGAAAAGTGGTATTCCCGAAGTTATCCGGCGTCTTTCCCTGACTAAGAGAGACGAAGCCGATCTAAACGCAGTAGAC
TCTGAGGGTAAAATTGCCACTGAGGAAACCAAAATCTCAGCGGAAGAAGATAAAAAGGAAACTAATGACGGGAAGACTTTTAAGGACTGGGCTGTGTGGAATCCCCTGAATTTGGTTAAGAACAGTTTAGAGAAACAATATAATCAGAGCCAGGGTGCACACTTACCAGCATTAGTTGTAGAGCCTGCCTTTAAGGGCAG
GATCATTTTATTTTCCTGTTCGGAGAGCCAGCCATGCCGAGCAGCTAGATCTTTCTTGAGACAAAAAGGACTCAAATTTGTCGAAATCAACATTGACATTTATCCCGGCAGGAAGACGGAGCTAGAAAACATAGCAGGTTCTTCATCTGTTCCAAAGATTTTCTTTAATGAATTGTGCTTGGGAGGGATGAATGAAGTTA
GGGCCATGGAAGAGTCTGGCGAACTCGATGAAAAGATCAAGGGATTGATTGAAACCGAGCCTCCTTCTTCGGCCCCTTTGCCACCGTCTGCAGGGGAAGATGATTTCGGGAACAATGGGATGGTGGATGAGTTTGCTAATGTTGTCAGAAAACTCCGGGAAGCAGTGGTTGTCAAGGATAGGTTTTATAAAATGCGGATG
TTCACCAGGTGCTTTGTTGGATCGGAAGCGGTCGATTTCTTGTCAGAGGATCAGTTGCTGGAGAGGGATGAGGCAGTTGAATTTGGACGAAAGCTCGCTTCAAAACATTTTTTCCACCATGGTCTAAATGAGAATGTCTTCGAAGACGGAAATCATCCTTATCGTTTCATGGAACATGATCCGGTTGTTTCCGCCAACTG
CTATAATTTTACTGGATGTACAAATGACATGAAGCCCAAACCTCCAGCTGAAATTGCAGCTAGACTGAGGAGCCTGACCCAAGCAATTTATGAAGCTTACATCTCTGATGATGGGAAGCATGTAGATTACAGAAGCATTGGTGCCAGTGAAGAGTTTATAAGGTACTTGAAAGTGATTGAGGAACTTCACAGAATTGATT
TACATGACTTATCCAGAGAAGAAAAACTTGCATTCTTCATCAATCTGTATAATATGATGGCAATTCATGCAATTGTGCTGTGGGGTTACCCTGATGGACCTCTGGAGAGGAGAAGATTTTTTGGTGAATTTAAATATGTCATTGGTGGCTATTCTTATTCACTTTCAGCCATTCAAAATGGAGTTTTGCGCAGTAACAAA
AGACCCCCTTACAATTTGATTAAACCTTTTGGGTTAAAAGACAAACGCATCGAGGTTGCCTTATCAGATCCAGAACCTTTGGTTCATTTTGCCTTGGTGTGTGGTTCAAGATCAAGCCCTGCCATCAGATGCTATTCGCCTGGAAGTATTGATGAAGAACTAAGGCTAGCTGGAAGGATATTTTTTGATGATGGTGGTTT
CTTGATTGATGTGGAGAACAAGCTTGCTTCAGTTAGCAAGATTATGAATTGGTACAGTGTGGACTTTGGCAAAAACGAAACAGAAGTCATGAAGTTTATTGCAAACTATTTGGAACCCTCCAAGTCAGAACAGCTGTTGGAATTATTGAATGGTAATCAACTGAAGGTCACATACCACAGTTATGATTGGGCTTTGAATT
GCTAAGTCCAATGTTTTTTTTTGACAAGGAATTGCTAAGTCCAATGTTACCTGTCATGCCCTAGATCAATTCATAGTCATCTATCAAATGGGATCTGTATCCCAATTTTATTGGGATGGAAGCTGAATTATTATGAAAGTCTGGAATTTTGCTGATGGTTGTGAGATAGAAGATCAAACGATCTGTTTACTAAGTTTTGG
TGCAAAGTCTTGTGAATAAGTAAGAAACACGGACCATTTTTGTTTTTGAAGTACTGGAAAGTCTGCGGTTCAAGCCCTTCCAAGCTGTTTGGTAAATGTGGCACGCCATTTTATTATGTTACTTCTTCACCGATTTATTAAAATATATTCTATAGCTATCTTGTCATTTGAACTGATCAATTTATTGGACTTCAAACTAG
TATGTCTTGAAGCTCTTTGGAAAATGTTAGAAGGAACTTGTTCCTCACATATGCATTTATTTCAATGCTAACTGGGAAACTTGTTTTGCTATATTTGTGAAACTTGATTATGTGAGCCTGGCCTTTTCTGCTAAATTTCACGTGTTCTCTAATTGATCATGCAGTGCATGTTTTGTAAAATTTAGGGTTTTTATGTAGAG
TTGTG

Intron 3 GTAAAAAGCT ... ATTCTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	18.18	72	16	1.8
A2	6.98	40	3	0.6
A3	11.9	37	5	0
A4	11.32	47	6	0.8
A5	11.11	16	2	0
A6	14.58	498	85	20.6
A7	14	431	70.2	12.6
A8	14.98	471	83	12.6
A9	14.06	359	58.7	11
A10	12.26	231	32.3	10.6

>TRINITY_DN47771_c1_g2_i6 from sample A7 / Example spliced isoform

GTTGCTCTTAAACATCCCGATTGCGCTGCGCTAGTCTTTATCTTTACTGAGTTGTCTTCTTAGAAATTTTTGTTTTTCTATGGTTCTTCATGGAAAATTTTGTTCATCCTTGTGGAGAATTCATTTAGGTTTTCCTTTTCCGGTTCTGTTTCGCTGTGTTTTCAGTTTAATAGCGGTGACAGTCGTTAGAATCTTCCATT
GCTTTTGGATTTAGGCATTTTCAGGAAGAATGACTCAGTGAGGATTTATTATGGTAGACAGACCATTTTATTAGAGAAGTATTGCCATTTCATTGTAGATTTGCGGAAAAAACAATTTCCGCCAAGAAAATCTAGTTCTGCGTTGTGAAATTTTGACTGTCTATTATTCGTTTATTGTTATTTTCTCTGTAGAAATCAAT
ATGGAAAACAAGGATTTCAAGGAGGAGCGATCTCAGGCAAATGATTCAGTTCCCGACGAGAAATTGACTTCTGAGAAACATGTTGATATTGAAGATCATAAAAATAATGTCGAACAAAAGAGTTCAGATATTGAAAAAGAGAGCACTGATGTAGAGAAGAATGAAGCTGATAAGGAGGATGGAGCCACGGTCGATCGAAC
CTTATACGTATGCGATGTTCCAGGCGAAGAAAAAGAAACTGAGCCTGTTTTCTACGGAACTGAAAATCCTGAAGCCGAAATTGGACGATCTCCAGAATCCGATTTCGGTTTAAGGGGGGCTGCTTGGCCGGAAAAGGCAACGGCTATAAAGAACTTCTTCATGGAGCGCGGCGTCATGATCCGGAAGTTTTCCGAGAAAA
GTGGTATTCCCGAAGTTATCCGGCGTCTTTCCCTGACTAAGAGAGACGAAGCCGATCTAAACGCAGTAGACTCTGAGGGTAAAATTGCCACTGAGGAAACCAAAATCTCAGCGGAAGAAGATAAAAAGGAAACTAATGACGGGAAGACTTTTAAGGACTGGGCTGTGTGGAATCCCCTGAATTTGGTTAAGAACAGTTTA
GAGAAACAATATAATCAGAGCCAGGGTGCACACTTACCAGCATTAGTTGTAGAGCCTGCCTTTAAGGGCAGGATCATTTTATTTTCCTGTTCGGAGAGCCAGCCATGCCGAGCAGCTAGATCTTTCTTGAGACAAAAAGGACTCAAATTTGTCGAAATCAACATTGACATTTATCCCGGCAGGAAGACGGAGCTAGAAAA
CATAGCAGGTTCTTCATCTGTTCCAAAGATTTTCTTTAATGAATTGTGCTTGGGAGGGATGAATGAAGTTAGGGCCATGGAAGAGTCTGGCGAACTCGATGAAAAGATCAAGGGATTGATTGAAACCGAGCCTCCTTCTTCGGCCCCTTTGCCACCGTCTGCAGGGGAAGATGATTTCGGGAACAATGGGATGGTGGATG
AGTTTGCTAATGTTGTCAGAAAACTCCGGGAAGCAGTGGTTGTCAAGGATAGGTTTTATAAAATGCGGATGTTCACCAGGTGCTTTGTTGGATCGGAAGCGGTCGATTTCTTGTCAGAGGATCAGTTGCTGGAGAGGGATGAGGCAGTTGAATTTGGACGAAAGCTCGCTTCAAAACATTTTTTCCACCATGGTCTAAAT
GAGAATGTCTTCGAAGACGGAAATCATCCTTATCGTTTCATGGAACATGATCCGGTTGTTTCCGCCAACTGCTATAATTTTACTGGATGTACAAATGACATGAAGCCCAAACCTCCAGCTGAAATTGCAGCTAGACTGAGGAGCCTGACCCAAGCAATTTATGAAGCTTACATCTCTGATGATGGGAAGCATGTAGATTA
CAGAAGCATTGGTGCCAGTGAAGAGTTTATAAGGTACTTGAAAGTGATTGAGGAACTTCACAGAATTGATTTACATGACTTATCCAGAGAAGAAAAACTTGCATTCTTCATCAATCTGTATAATATGATGGCAATTCATGCAATTGTGCTGTGGGGTTACCCTGATGGACCTCTGGAGAGGAGAAGATTTTTTGGTGAAT
TTAAATATGTCATTGGTGGCTATTCTTATTCACTTTCAGCCATTCAAAATGGAGTTTTGCGCAGTAACAAAAGACCCCCTTACAATTTGATTAAACCTTTTGGGTTAAAAGACAAACGCATCGAGGTTGCCTTATCAGATCCAGAACCTTTGGTTCATTTTGCCTTGGTGTGTGGTTCAAGATCAAGCCCTGCCATCAGA
TGCTATTCGCCTGGAAGTATTGATGAAGAACTAAGGCTAGCTGGAAGGATATTTTTTGATGATGGTGGTTTCTTGATTGATGTGGAGAACAAGCTTGCTTCAGTTAGCAAGATTATGAATTGGTACAGTGTGGACTTTGGCAAAAACGAAACAGAAGTCATGAAGTTTATTGCAAACTATTTGGAACCCTCCAAGTCAGA
ACAGCTGTTGGAATTATTGAATGGTAATCAACTGAAGGTCACATACCACAGTTATGATTGGGCTTTGAATTGCTAAGTCCAATGTTACCTGTCATGCCCTAGATCAATTCATAGTCATCTATCAAATGGGATCTGTATCCCAATTTTATTGGGATGGAAGCTGAATTATTATGAAAGTCTGGAATTTTGCTGATGGTTGT
GAGATAGAAGATCAAACGATCTGTTTACTAAGTTTTGGTGCAAAGTCTTGTGAATAAGTAAGAAACACGGACCATTTTTGTTTTTGAAGTACTGGAAAGTCTGCGGTTCAAGCCCTTCCAAGCTGTTTGGTAAATGTGGCACGCCATTTTATTATGTTACTTCTTCACCGATTTATTAAAATATATTCTATAGCTATCTT
GTCATTTGAACTGATCAATTTATTGGACTTCAAACTAGTATGTCTTGAAGCTCTTTGGAAAATGTTAGAAGGAACTTGTTCCTCACATATGCATTTATTTCAATGCTAACTGGGAAACTTGTTTTGCTATATTTGTGAAACTTGATTATGTGAGCCTGGCCTTTTCTGCTAAATTTCACGTGTTCTCTAATTGATCATGC
AGTGCATGTTTTGTAAAATTTAGGGTTTTTATGTAGAGTTGTGCTAAGTAAGATG

>TRINITY_DN47771_c1_g2_i3 from sample A7 / Example unspliced isoform:

CCCGCGTAAATCTAAGCGACTGCCATTTACTTTTCCCGCCCGGAAGAATTTGTCCCGGTCCGCGTGCATAATTTTCTACAAAATCTGTATAAATAGGACTTGGTCGCCAAAGACTGCCGGACTGCCAGCGGCCGTTTAACGGACTATTTGTGAGTGTATCGTTATTCTTGCTACGGCTTCGGATTCTGCGAATCGCGGCG
AAAACGTAAATCAATATGGAAAACAAGGATTTCAAGGAGGAGCGATCTCAGGCAAATGATTCAGTTCCCGACGAGAAATTGACTTCTGAGAAACATGTTGATATTGAAGATCATAAAAATAATGTCGAACAAAAGAGTTCAGATATTGAAAAAGAGAGCACTGATGTAGAGAAGAATGAAGCTGATAAGGAGGATGGAGC
CACGGTCGATCGAACCTTATACGTATGCGATGTTCCAGGCGAAGAAAAAGAAACTGAGCCTGTTTTCTACGGAACTGAAAATCCTGAAGCCGAAATTGGACGATCTCCAGAATCCGATTTCGGTTTAAGGGGGGCTGCTTGGCCGGAAAAGGCAACGGCTATAAAGAACTTCTTCATGGAGCGCGGCGTCATGATCCGGA
AGTTTTCCGAGAAAAGTGGTATTCCCGAAGTTATCCGGCGTCTTTCCCTGACTAAGAGAGACGAAGCCGATCTAAACGCAGTAGACTCTGAGGGTAAAATTGCCACTGAGGAAACCAAAATCTCAGCGGAAGAAGATAAAAAGGAAACTAATGACGGGAAGACTTTTAAGGACTGGGCTGTGTGGAATCCCCTGAATTTG
GTTAAGAACAGTTTAGAGAAACAATATAATCAGAGCCAGGGTGCACACTTACCAGCATTAGTTGTAGAGCCTGCCTTTAAGGGCAGGATCATTTTATTTTCCTGTTCGGAGAGCCAGCCATGCCGAGCAGCTAGATCTTTCTTGAGACAAAAAGGACTCAAATTTGTCGAAATCAACATTGACATTTATCCCGGCAGGAA
GACGGAGCTAGAAAACATAGCAGGTTCTTCATCTGTTCCAAAGATTTTCTTTAATGAATTGTGCTTGGGAGGGATGAATGAAGTTAGGGCCATGGAAGAGTCTGGCGAACTCGATGAAAAGATCAAGGGATTGATTGAAACCGAGCCTCCTTCTTCGGCCCCTTTGCCACCGTCTGCAGGGGAAGATGATTTCGGGAACA
ATGGGATGGTGGATGAGTTTGCTAATGTTGTCAGAAAACTCCGGGAAGCAGTGGTTGTCAAGGATAGGTTTTATAAAATGCGGATGTTCACCAGGTGCTTTGTTGGATCGGAAGCGGTCGATTTCTTGTCAGAGGATCAGTTGCTGGAGAGGGATGAGGCAGTTGAATTTGGACGAAAGCTCGCTTCAAAACATTTTTTC
CACCATGGTCTAAATGAGAATGTCTTCGAAGACGGAAATCATCCTTATCGTTTCATGGAACATGATCCGGTTGTTTCCGCCAACTGCTATAATTTTACTGGATGTACAAATGACATGAAGCCCAAACCTCCAGCTGAAATTGCAGCTAGACTGAGGAGCCTGACCCAAGCAATTTATGAAGCTTACATCTCTGATGATGG
GAAGCATGTAGATTACAGAAGCATTGGTGCCAGTGAAGAGTTTATAAGGTACTTGAAAGTGATTGAGGAACTTCACAGAATTGATTTACATGACTTATCCAGAGAAGAAAAACTTGCATTCTTCATCAATCTGTATAATATGATGGCAATTCATGCAATTGTGCTGTGGGGTTACCCTGATGGACCTCTGGAGAGGAGAA
GATTTTTTGGTGAATTTAAATATGTCATTGGTGGCTATTCTTATTCACTTTCAGCCATTCAAAATGGAGTTTTGCGCAGTAACAAAAGACCCCCTTACAATTTGATTAAACCTTTTGGGTTAAAAGACAAACGCATCGAGGTTGCCTTATCAGATCCAGAACCTTTGGTTCATTTTGCCTTGGTGTGTGGTTCAAGATCA
AGCCCTGCCATCAGATGCTATTCGCCTGGAAGTATTGATGAAGAACTAAGGCTAGCTGGAAGGATATTTTTTGATGATGGTGGTTTCTTGATTGATGTGGAGAACAAGCTTGCTTCAGTTAGCAAGATTATGAATTGgtaaaaagcttcaagacaatttcattgtctccttgtagaatatgaacactattgagtgtctgc
ttacctgaaacctaattcttgcagGTACAGTGTGGACT