sp|Q9FJL0|SMC4_ARATH ----> Structural maintenance of chromosomes protein 4

Intron 1 GTTGGTTTTG ... GCACATGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	40	9	6	3.3
A2	30	7	3	2.3
A3	44.44	5	4	3.3
A4	0	1	0	0.6
A5	33.33	4	2	1.2
A6	0	1	0	0.6
A7	18.75	13	3	1.8
A8	25.58	32	11	10
A9	13.33	13	2	7.8
A10	15.79	16	3	6.8

>TRINITY_DN126351_c2_g1_i3 from sample A1 / Example spliced isoform

ATGCATACCTTACCTGATGACTTACCTGAATTGGCAGGAACTGTTTTCCTTGAATTATCATTCCATTCCTAGCTAACCATAAAACCCATAAAACCCATGCAACTGTACAGGGAAAGCCTTGTGATCTGTAACTGCTCTGTCCAAACACCAATTTAAGCAATCAGAGATAGATTCTTCTTCCCATTCCCCTTGACATTAAT
TAGTTTTAGACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTT
CCATATTACCTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTT
CTTTCCTGATCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCA
ATTCCATGTGCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGG
GGTGAGTGTAATTCTTCTGTCAAGTTGGTCATATATTTGTTAATGTCAAGTTGGTTGTTGAAAATTCATAAGCTGCTTGTGCGAACCTCCCAAGCCACCATGAGAACATGGTTGTCTAATCAGCATGGAGTTACATTTATGCCTTTAGCTTCTCCTGGCCAAAATATGTTGTATAGTGAATGAACTGAGAAGCCATGTTA
ACCCCTCTTCAATTGTCAGGTTTACAGAAAAATGGGATCAATTCCACAAGAGGAAGGTAAGATGTCTCCAGTTTTAGGAAACTTTGAAGTTTCAATACAGAAAAAAAAATCTTTCTAGCACAGGCAGAGAAGAAACAATCTTCTATATAAATATATATTGTATTTGCATAGCTGGTACAGCTCTATATAGAACTGTACAG
ATTTTATGTACTCTGTTTTGAATAATGTCTCATAGATCCTGTTTGGGTCTTCCAAGGACAATAATAAAAAAATCATTAATTCATATGCATTTTTTCTCTATCCTTGCTGCTCACATTTTTATTTTTTTTCTTAATTTGGGCAGTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGT
GACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGC
AAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTGCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTA
AATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACAT
TTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGTGGAAA
TGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCTGCAACCACA
TTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGTCTTCCAAAA
ATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAG
ATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGA
TCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCT
TAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAAAAGTTTCTCAGCGCGAATGAACAATTTCATGAAGCAGAACTTCAAATGT
CTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGT
AGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGA
ACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAA
ATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACT
TCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTCTTGAGATCGCTCCTTCA
CGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGC

>TRINITY_DN126351_c2_g1_i7 from sample A1 / Example unspliced isoform:

ATGCATACCTTACCTGATGACTTACCTGAATTGGCAGGAACTGTTTTCCTTGAATTATCATTCCATTCCTAGCTAACCATAAAACCCATAAAACCCATGCAACTGTACAGGGAAAGCCTTGTGATCTGTAACTGCTCTGTCCAAACACCAATTTAAGCAATCAGAGATAGATTCTTCTTCCCATTCCCCTTGACATTAAT
TAGTTTTAGACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTT
CCATATTACCTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTT
CTTTCCTGATCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCA
ATTCCATGTGCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGG
GGTGAGTGTAATTCTTCTGTCAAGTTGGTCATATATTTGTTAATGTCAAGTTGGTTGTTGAAAATTCATAAGCTGCTTGTGCGAACCTCCCAAGCCACCATGAGAACATGGTTGTCTAATCAGCATGGAGTTACATTTATGCCTTTAGCTTCTCCTGGCCAAAATATGTTGTATAGTGAATGAACTGAGAAGCCATGTTA
ACCCCTCTTCAATTGTCAGGTTTACAGAAAAATGGGATCAATTCCACACGAGGAAGGTAAGATGTCTCCAGTTTTAGGAAACTTTGAAGTTTCAATACAGAAAAAAAAATCTTTCTAGCACAGGCAGAGAAGAAACAATCTTCTATATAAATATATATTGTATTTGCATAGCTGGTACAGCTCTATATAGAACTGTACAG
ATTTTATGTACTCTGTTTTGAATAATGTCTCATAGATCCTGTTTGGGTCTTCCAAGGACAATAATAAAAAAATCATTAATTCATATGCATTTTTTCTCTATCCTTGCTGCTCACATTTTTATTTTTTTTCTTAATTTGGGCAGTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGT
GACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGC
AAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTGCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTA
AATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACAT
TTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGTGGAAA
TGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCTGCAACCACA
TTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGTCTTCCAAAA
ATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAG
ATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGA
TCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCT
TAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAAAAGTTTCTCAGCGCGAATGAACAATTTCATGAAGCAGAACTTCAAATGT
CTACCAGgttggttttggataattttaatgatgccagtttatgatagttgactggttttcttccaacaattaaaagaaaatatggattggcatcatataactagccatttttttgcaagatgaatgttttcttatttaaaactccactaaggaacacttgaagaatgcacatgcagGAAAACAGAAATTGAGAAAATGAA
AGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATG
AACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCA
CAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTG
GCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGC
CTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGA
TTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGC

Intron 2 GTACTGGCAA ... TATGCTGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	77.78	2	7	7
A2	42.93	6.7	6	4
A3	55.56	2	4	1
A4	20.67	8	2	2.3
A5	20.64	3	1	0.7
A6	-1	0	0	0
A7	29.67	7	4	2
A8	20	2	0	1
A9	36.45	9	8	2.3
A10	28.12	14	9	2

>TRINITY_DN106847_c0_g1_i1 from sample A2 / Example spliced isoform

ATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGA
AAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACT
TGAAACTGGATGACTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGCATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGCTGTACAGGAACGACTAAACATCTCAAA
TGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGA
TTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCAT
CTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAA
TTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTA
GTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTT
TCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATT
GAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAGAAGTTTCTCAGCGCGAAGGAACAATTTC
ATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTT
TTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAA
TGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGGTAAGTTTGCGCTAGTTGCTCTGATTGATTTTCTATTAGGGACGCACTTTTTATGTTTCATACTAATTATTTCAAGTTTTTA
GCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTCACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTT
TACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGT
ATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGCACCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGCAGTTACATTCTCTCTTGCAAATGATCCA
TTCAACTACAACAAAGTATTATAACATTGAAGTTCACAACCAACACAGTCAAAACTAAATACAAGTAACATAGAATCATACATGCACAGTTTTGGACCAACGTACACATTAGAACTCCTTTGGTTCAGGTTAGATAATTGCACA

>TRINITY_DN106847_c0_g1_i7 from sample A2 / Example unspliced isoform:

ATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTACAAATTACAAGAATATC
AGCCTTCCAGATTTCTTCTAAGCCTAACATTTTGTAATAAGATTAGATCATCATATGGGTGTTTTCCTTAAACTAGCTTTACTTCTGGAAAATAATTCCTGAAGTGGACATGCTATGTATGTACTATGAATCCTTACAGGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAAC
AAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGACTCTACTGTCCAAGAGGAAGCTTTCCTT
ACCATGAAGATTGCAAGAATGCAGGCATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGgtactggcaatggatatattctagaaactgctttttatacaagaaaatctaatactagtgccatatgct
gaagCTGTACAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATTGGAGGTAATGTTTAGATTACTGATTTAGAAAAACTATTTTTATAAGTCAAGAAACCATACTGTGATGGCTTCCTTAAATGATTATGGTCCTCGTTTCCCAGAAGAGATATCTGTGATGCAGCA
GCAAC

Intron 3 GTACAAATTA ... ATCCTTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	55.56	6	9	6
A2	46.67	8	7	7
A3	54.29	8	13	6
A4	44.44	5	4	4
A5	60	3	6	3
A6	100	0	0	1
A7	42.86	2	2	1
A8	50	2	1	3
A9	20	6	3	0
A10	42.86	2	1	2

>TRINITY_DN106847_c0_g1_i1 from sample A2 / Example spliced isoform

ATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGA
AAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACT
TGAAACTGGATGACTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGCATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGCTGTACAGGAACGACTAAACATCTCAAA
TGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGA
TTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCAT
CTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAA
TTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTA
GTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTT
TCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATT
GAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAGAAGTTTCTCAGCGCGAAGGAACAATTTC
ATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTT
TTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAA
TGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGGTAAGTTTGCGCTAGTTGCTCTGATTGATTTTCTATTAGGGACGCACTTTTTATGTTTCATACTAATTATTTCAAGTTTTTA
GCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTCACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTT
TACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGT
ATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGCACCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGCAGTTACATTCTCTCTTGCAAATGATCCA
TTCAACTACAACAAAGTATTATAACATTGAAGTTCACAACCAACACAGTCAAAACTAAATACAAGTAACATAGAATCATACATGCACAGTTTTGGACCAACGTACACATTAGAACTCCTTTGGTTCAGGTTAGATAATTGCACA

>TRINITY_DN106847_c0_g1_i7 from sample A2 / Example unspliced isoform:

ATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGgtacaaattacaagaatatc
agccttccagatttcttctaagcctaacattttgtaataagattagatcatcatatgggtgttttccttaaactagctttacttctggaaaataattcctgaagtggacatgctatgtatgtactatgaatccttacagGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAAC
AAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGACTCTACTGTCCAAGAGGAAGCTTTCCTT
ACCATGAAGATTGCAAGAATGCAGGCATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGGTACTGGCAATGGATATATTCTAGAAACTGCTTTTTATACAAGAAAATCTAATACTAGTGCCATATGCT
GAAGCTGTACAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATTGGAGGTAATGTTTAGATTACTGATTTAGAAAAACTATTTTTATAAGTCAAGAAACCATACTGTGATGGCTTCCTTAAATGATTATGGTCCTCGTTTCCCAGAAGAGATATCTGTGATGCAGCA
GCAAC

Intron 4 GCAAGAATTC ... TTTTCTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	19.23	21	5	5
A2	26.32	7	4	1
A3	18.92	15	0	7
A4	7.69	12	1	1
A5	-1	0	0	0
A6	41.18	5	5	2
A7	20	18	2	7
A8	21.95	48	8	19
A9	15.91	37	6	8
A10	24.53	20	7	6

>TRINITY_DN45892_c0_g1_i3 from sample A10 / Example spliced isoform

GAACATGAATTCCTTCAATTTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAAC
ATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAG
AAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCA
ATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGCTGTACAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATTGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACA
AGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAA
GTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTAC
AATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGAT
GGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAA
GCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAAC
AGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTAT
AAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAGAAGTTTCTCAGCGCGAAGGAACAATTTCATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGA
GGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGG
AGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAAT
CGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTTTACAAGC
AATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTG
TCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGCAGTTACATTCTCTCTTGCAAATGATCCATTCAACT
ACAGCAAAGTATTATAACATTGAAGTTCACAACCAACACAGTCAAAACTAAATATAAGTAACATAGA

>TRINITY_DN45892_c0_g1_i1 from sample A10 / Example unspliced isoform:

GAACATGAATTCCTTCAATTTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAAC
ATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAG
AAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCA
ATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGCTGTACAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATTGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACA
AGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAA
GTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTAC
AATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGAT
GGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAA
GCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAAC
AGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTAT
AAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAGAAGTTTCTCAGCGCGAAGGAACAATTTCATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGA
GGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGG
AGGAGATGTCTCTGAATGAAATCAGAAGgcaagaattcatttagcaaacatttttttgcagttggactagggcaatgactaactgaaacgtacgtggtggtttgctttcattgattcattatttctgaaacgtgtttgttttctacagGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAA
TCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCT
TTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAAT
ACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTC
TTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGCAGTTACATTCTCTCTTGCAAATGATCCATTCAACTACAGCAAAGTATTATAACATTGAAGTTCACAACCAACACAGTCAAAACTAAATATAAGTAACATAGA

Intron 5 GTAAGTTTGC ... AAGTTTTTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	24.72	19.1	4.5	6.3
A2	25	12	11.4	4
A3	24.56	12.4	4.5	4
A4	25	6	5.9	2
A5	33.33	2	1.3	1
A6	0	5	3.2	0
A7	11.52	43.3	11.6	5.6
A8	26.53	46.1	16.2	16.6
A9	12.29	45.1	11.6	6.4
A10	18.17	36.1	11.3	8

>TRINITY_DN106847_c0_g1_i5 from sample A2 / Example spliced isoform

ATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGA
AAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACT
TGAAACTGGATGACTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGCATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGCTGTACAGGAACGACTAAACATCTCAAA
TGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGA
TTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCAT
CTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAA
TTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTA
GTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTT
TCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATT
GAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAGAAGTTTCTCAGCGCGAAGGAACAATTTC
ATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTT
TTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAA
TGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTCACAGAGGAAAAGAGTC
TCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCA
GAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGCA
CCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGCAGTTACATTCTCTCTTGCAAATGATCCATTCAACTACAACAAAGTATTATAACATTGAAGTTCACAACCAACACAGTCAAAACTAAATACAAGTAACATAGAATCATACAT
GCACAGTTTTGGACCAACGTACACATTAGAACTCCTTTGGTTCAGGTTAGATAATTGCACA

>TRINITY_DN106847_c0_g1_i1 from sample A2 / Example unspliced isoform:

ATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGA
AAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACT
TGAAACTGGATGACTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGCATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGCTGTACAGGAACGACTAAACATCTCAAA
TGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGA
TTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCAT
CTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAA
TTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTA
GTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTT
TCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATT
GAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAGAAGTTTCTCAGCGCGAAGGAACAATTTC
ATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTT
TTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAA
TGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGgtaagtttgcgctagttgctctgattgattttctattagggacgcactttttatgtttcatactaattatttcaagttttta
gCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTCACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTT
TACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGT
ATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGCACCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGCAGTTACATTCTCTCTTGCAAATGATCCA
TTCAACTACAACAAAGTATTATAACATTGAAGTTCACAACCAACACAGTCAAAACTAAATACAAGTAACATAGAATCATACATGCACAGTTTTGGACCAACGTACACATTAGAACTCCTTTGGTTCAGGTTAGATAATTGCACA

Intron 6 GTATCTGATC ... GGGTTAGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	56.76	8	6	15
A2	100	0	7	4
A3	51.72	7	10	5
A4	76.47	2	7	6
A5	-1	0	0	0
A6	33.33	1	0	1
A7	77.78	1	2	5
A8	100	0	6	4
A9	47.37	5	3	6
A10	100	0	17	13

>TRINITY_DN105961_c0_g1_i2 from sample A3 / Example spliced isoform

CAACGGCACCGGCAAAAGCGTATCCATTTTCATGATTAAAAATAAGAGTCCTTTAGACCAAATAATTCGTAGAAAGATGAATTCTCTTAACCAATTCAATTGCAGGTCATCGGCGAAGCCCTGGCATTTGCACTGGGGGCATCGCCCAAAGTCCTAAGGGTCGATGCATTTTCTTCGCTCGTCAATCATCGTTCGGCTTC
GGCTTCATCTTCTGCCAAGGTGAGTGTAGGGTTCGAACGAAGGGATGGCGGTGAGAAGGTGAAGATCTATAGGGTTTTGTCCGGGTCCTCTACTAAATTCTACTGGAAAGATGATAATCAAACCCCGAAGAAGGAAATTTCCTTATCCGAGTTGAAACAGAAGCTAGCTAGTTTCAGTATCCCCGCTAATAATCTAGATA
GGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTC
AGCCCTGAAGTTGAAAAATGGAAGGGGTGAGTGTAATTCTTCTGTCAAGTTGGTCATATATTTGTTAATGTCAAGTTGGTTGTTGAAAATTCATAAGCTGCTTGTGCGAACCTCCCAAGCCACCATGAGAACATGTTTGTCTAATCAGCATGGAGTTACATTTATGCCTTTAGCTTCTCCTGGCCAAAATATGTTGTATA
GTGAATGAACTGAGAAGCCATGTTAACCCCTCTTCAATTGTCAGGTTTACAGAAAAATGGGATCAATTCCACAAGAGGAAGTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGTGACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTAC
AACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATG
ATCAAAGAAGAGGTACAAATTACAAGAATATCAGCCTTCCAGATTTCTTCTAAGCCTAACATTTTGTAATAAGATTAGATCATCATTTGGGTGTTTTCCTTAAACTAGCTTTACTTC

>TRINITY_DN105961_c0_g1_i7 from sample A3 / Example unspliced isoform:

CTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTTCCATATTACCTTCCACCACCATTTC
CTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTTCTTTCCTGATCCAATCCTCTACAGA
CCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGgtatctgatcttaaaactgtgcttaatttgcaattccatgtgctatgtctaaatatt
cagggttagcagCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGGGGTGAGTGTAATTCTTCTGTCAAGT
TGGTCATATATTTGTTAATGTCAAGTTGGTTGTTGAAAATTCATAAGCTGCTTGTGCGAACCTCCCAAGCCACCATGAGAACATGTTTGTCTAATCAGCATGGAGTTACATTTATGCCTTTAGCTTCTCCTGGCCAAAATATGTTGTATAGTGAATGAACTGAGAAGCCATGTTAACCCCTCTTCAATTGTCAGGTTTAC
AGAAAAATGGGATCAATTCCACAAGAGGAAGTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGTGACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGCCAAATTG
TTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTACAAATTACAAGAATATCAGCCTTCCAGATTTCTTC
TAAGCCTAACATTTTGTAATAAGATTAGATCATCATTTGGGTGTTTTCCTTAAACTAGCTTTACTTC

Intron 7 GTCATTCTCG ... GCAACTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	50	4	4	4
A2	23.08	5	3	0
A3	43.59	11	12	5
A4	0	3	0	0
A5	0	3	0	0
A6	50	4	5	3
A7	20	4	2	0
A8	-1	0	0	0
A9	40	3	3	1
A10	28.57	5	4	0

>TRINITY_DN105961_c0_g1_i5 from sample A3 / Example spliced isoform

CAACGGCACCGGCAAAAGCGTATCCATTTTCATGATTAAAAATAAGAGTCCTTTAGACCAAATAATTCGTAGAAAGATGAATTCTCTTAACCAATTCAATTGCAGGTCATCGGCGAAGCCCTGGCATTTGCACTGGGGGCATCGCCCAAAGTCCTAAGGGTCGATGCATTTTCTTCGCTCGTCAATCATCGTTCGGCTTC
GGCTTCATCTTCTGCCAAGGTGAGTGTAGGGTTCGAACGAAGGGATGGCGGTGAGAAGGTGAAGATCTATAGGGTTTTGTCCGGGTCCTCTACTAAATTCTACTGGAAAGATGATAATCAAACCCCGAAGAAGGAAATTTCCTTATCCGAGTTGAAACAGAAGCTAGCTAGTTTCAGTATCCCGGCGAATAATCTAGATA
GGTGATACTTTTTCATTTTTTTCTTGATTATTATTTTTATTTGAGCATTACAATTAAGCTAAATTTTAATTACTAATTTTGAAACGAACAACGACAAATATATATAGTTGTAATTTCTAAATATTTTTAAATTT

>TRINITY_DN105961_c0_g1_i8 from sample A3 / Example unspliced isoform:

CAACGGCACCGGCAAAAGCGTATCCATTTTCATGATTAAAAATAAGAGTCCTTTAGACCAAATAATTCGTAGAAAGATGAATTCTCTTAACCAATTCAATTGCAGGTCATCGGCGAAGCCCTGGCATTTGCACTGGGGGCATCGCCCAAAGTCCTAAGGGTCGATGCATTTTCTTCGCTCGTCAATCATCGTTCGGCTTC
GGCTTCATCTTCTGCCAAGgtcattctcgtctgaattcatcttttcttttcttccctttgttaagaaatatataggtgaatacacagttcaagggcaactgcagGTGAGTGTAGGG

Intron 8 GTATGCCATG ... AAATCAGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	57.38	13	14	21
A2	93.55	1	22	7
A3	64.1	7	10	15
A4	100	0	7	12
A5	52.38	5	11	0
A6	66.67	3	7	5
A7	60.49	16	31	18
A8	61.49	31	51	48
A9	69.23	18	44	37
A10	78.26	5	16	20

>TRINITY_DN48232_c0_g1_i9 from sample A7 / Example spliced isoform

CTGACCTTAATGTCAACATTAATTTATTACCTTTATATGTTGCATTTTTAAGTTGCTTAACATTGTTATAATATTCACCCTATGCTAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGA
CCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGAT
ACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGAT
CCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAGAAGTTTCTCAGCGCGAAGGAACAATTTCATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAG
CAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGAACATTCGTGC
CGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATG
GAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTTT

>TRINITY_DN48232_c0_g1_i5 from sample A7 / Example unspliced isoform:

AAATAAAGAATACCACAAAATCCACAAATGCCTGGGTTTCCTTGACTTGCTCCTTCAAAGTATCCCCAGGCTTTCGTGTAATCAATATCTGGGAGTTTCAAGATTCTTGGAGTTTTTGCCTTTGCTAGCTTCCATATTCCATGATATGCATACCTTACCTGATGACTTACCTGAATTGGCAGGAACTGTTTTCCTTGAAT
TATCATTCCATTCCTAGCTAACCATAAAACCCATAAAACCCATGCAACTGTACAGGGAAAGCCTTGTGATCTGTAACTGCTCTGTCCAAACACCAATTTAAGCAATCAGAGATAGATTCTTCTTCCCATTCCCCTTGACATTAATTAGTTTTAGACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGAT
GGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTTCCATATTACCTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTT
GCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTTCTTTCCTGATCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTAC
CTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCAATTCCATGTGCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATC
GGAACCGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGGGGTTTACAGAAAAATGGGATCAATTCCACAAGAGGAAGTCACTATTTCTCAGACG
CCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGTGACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACA
AATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAA
AGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGACTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGG
AATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGCTGTACAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATTGGAGATTCATATCTCAAAGAA
GGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAG
ATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATAT
TTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAAC
CACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGA
AGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAA
GTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAG
ATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAGAAGTTTCTCAGCGCGAAGGAACAATTTCATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTG
AATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGgtatgccatgaactgtctaatccg
tcttttgaagcacttgcaaatgaagcagaagatgaggaaggcctgatcttggctcaggaggagatgtctctgaatgaaatcagaagGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAA
GGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATT
CCCTATCCGGGGGACAACAAGCTCTAGCCTCTTTAGCCTTGTCATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGAT
CTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCA
TGTGCACATTTATGAAAAGTAGCAGTTACATTCTCTCTTGCAAATGATCCATTCAACTACAACAAAGTATTATAACATTGAAGTTCACAACCAACACAGTCAAAACTAAATACAAGTAACATAGAATCATACATGCACAGTTTTGGACCAACGTACACATTAGAACTCCTTTGGTTCAGGTTAGATAATTGCACAACCTT
AATTTTTTTTTGTACTTTGCTGGTAATTACTGCTAAAATAGCATGATTCATATTCTTTGAAATTTGATTAAATAAATC

Intron 9 GCAAGAATTC ... TTTTCTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	19.23	21	5	5
A2	26.32	7	4	1
A3	18.92	15	0	7
A4	7.69	12	1	1
A5	-1	0	0	0
A6	41.18	5	5	2
A7	20	18	2	7
A8	21.95	48	8	19
A9	15.91	37	6	8
A10	24.53	20	7	6

>TRINITY_DN45676_c0_g1_i18 from sample A8 / Example spliced isoform

GCCCGTATGAATTATTCCATTTAACAGGTGGAAATGAAACATTTGCTAAAGAAGCGACATGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAAGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGCGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTC
CATTCTTTGTCATCTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCC
AGTGTTCAGAAAATTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCA
GCATTTAAATCTAGTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAA
ATATCATTTGGTTTCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTG
AACTTGTTGAATTGAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAAAAGTTTCTCAGCGCG
AATGAACAATTTCATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATT
GAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAA
AGTACCGAAAGAATGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACA
GAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGC
ACGGCTAGTTGCAGAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCT
CAGAATGATGGAACCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGCAGTTACATTCTCTCTTGCAAATGATCCATTCAACTACAACAAAGTATTATAACATTGAAGTTCACAACCAACACAGTCAAAACTAAATACAAGTAACA
TAGAATCATACATGCACAGTTTTGGACCAACGTACACATTAGAACCCCTTTGGTTCAGGTTAGATAATTGCACAACCTTAATTTTTTTAAGTTGTACTTTGCTGGTAATTACTGCTAAAATAGCATGATTCATATTCTTTGAAATTTGATTAAATAAATCTCCGTTTTACTAACACATTATTTTAACAAGAGCCACAAAG
TGGCAATGTCCTGCGTCATTGCAAATTAGTTTTTTGAAATTTGCG

>TRINITY_DN45676_c0_g1_i10 from sample A8 / Example unspliced isoform:

ACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGAAAAG
GATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAA
ACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGGAACGACTAAACATCTCAAATGAGAGGAGGAG
AGACCACATTTCACGAGCTGCACAGTTAACATTGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATG
AGGTGGAAATGAAACATTTGCTAAAGAAGCGACATGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAAGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGCGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCT
GCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGT
CTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCT
TCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCA
GCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAAT
TAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAAAAGTTTCTCAGCGCGAATGAACAATTTCATGAAGCAGAAC
TTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAA
GACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGgcaagaattcatttagcaaacattttttttgcagttggactagggcaatgactaactgaa
acgtacgtggtggtttgctttcattgattcattatttctgaaacgtgtttgttttctacagGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTT
AATATCTTTACAAAATCTGTCAAAAAGGTAAGTTTGCGCTAGTTGCTCTGATTGATTTTCTATTAGGGACGCACTTTTTATGTTTCATACTAATTATTTCAAGTTTTTAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTT
TCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACAT
CAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTCTTGA
GATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGCAGTTACATTCTCTCTTGCAAATGATCCATTCAACTACAACAAAGTATTATAACATTGAAGTTCACAACCAACACAGTCAAAACTAAATACAAGTAACATAGAATCATACATGCACAGTT
TTGGACCAACGTACACATTAGAACCCCTTTGGTTCAGGTTAGATAATTGCACAACCTTAATTTTTTTAAGTTGTACTTTGCTGGTAATTACTGCTAAAATAGCATGATTCATATTCTTTGAAATTTGATTAAATAAATCTCCGTTTTACTAACACATTATTTTAACAAGAGCCACAAAGTGGCAATGTCCTGCGTCATTG
CAAATTAGTTTTTTGAAATTTGCG

Intron 10 GTGAGTGTAA ... ATCCTTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	50	8	10	6
A2	76.47	2	6	7
A3	45.45	12	14	6
A4	46.67	4	3	4
A5	63.64	2	4	3
A6	100	0	0	1
A7	52.38	5	10	1
A8	69.23	2	6	3
A9	60	1	3	0
A10	60	2	4	2

>TRINITY_DN96807_c0_g1_i1 from sample A4 / Example spliced isoform

ACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTTCCATATTAC
CTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTTCTTTCCTGA
TCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCAATTCCATGT
GCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGGGGTGCAGTT
GAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTGAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAG
GGTCAAATAACTTGAAACTGGATGACTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCAACACTCTCTCTCAAAGCTGTACAGGAACGACT
AAACATCTCAAATGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATTGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGC
TGAGAGAAGAGATTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCC
ATTCTTTGTCATCTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCA
GTGTTCAGAAAATTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAG

>TRINITY_DN96807_c0_g1_i6 from sample A4 / Example unspliced isoform:

ACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTTCCATATTAC
CTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTTCTTTCCTGA
TCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCAATTCCATGT
GCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGGGgtgagtgt
aattcttctgtcaagttggtcatatatttgttaatgtcaagttggttgttgaaaattcataagctgcttgtgcgaacctcccaagccaccatgagaacatggttgtctaatcagcatggagttacatttatgcctttagcttctcctggccaaaatatgttgtatagtgaatgaactgagaagccatgttaacacctctt
caattgtcaggtttacagaaaaatgggatcaattccacaagaggaaggtaagatgtctccagttttaggaaactttgaagtttcaatacagaaaaaaaaatctttctagcacaggcagagaagaaacaatcttctatataaatatatattgtatttgcatagctggtacagctctatatagaactgtacaaattttatgt
actctgttttgaatgatgtctcatagatcctgtttgggtcttccaaggacaataataaaaaaatcattaattcatatgcattttttctctatccttgctgctcacatttttattttttttcttaatttggtcagtcactatttctcagacgccaagagaaatccctgcatgcaaatttgcaaatatatagtgaccagaag
aaagagaaagaacatgaattccttcaaattcaaaacagcatcaatgtatctacaactttctctgcctttgctcattacagattgaatttactgagccaaattgttgtctttcttaaacatgttttattagactttacaagggtcattaacaaatttgaatctggagcacactgaattgcatactctcctgcaagagtgtc
aaagcaaacataaaattgcaaaaaaacaatatgattcgcaaaggattaaaatgatcaaagaagaggtacaaattacaagaatatcagccttccagatttcttctaagcctaacattttgtaataagattagatcatcatatgggtgttttccttaaactagctttacttctggaaaataattcctgaagtggacatgcta
tgtatgtactatgaatccttacagGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTTCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTGAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGAC
TGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGACTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAATGTCATAGTCTAATTGATTTCATACTTTCAGTTACGGTTACAAAGAAGCATGTGCAATCTCAGGTGTTTTTATTCAGATGCTTGTCCA
ACACTCTCTCTCAAAGCTGTACAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATTGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAAT
TGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGT

Intron 11 GTGAGTGTAA ... CAATTGTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	44.52	14	10	12.5
A2	46.85	6	6	4.6
A3	44.82	11	14	3.9
A4	74.55	1	3	2.9
A5	63.18	2	4	2.9
A6	100	0	0	4.8
A7	55.24	7	10	7.4
A8	85.41	1	6	5.8
A9	57.14	3	3	5
A10	37.82	4	4	0.9

>TRINITY_DN126351_c2_g1_i1 from sample A1 / Example spliced isoform

ATGCATACCTTACCTGATGACTTACCTGAATTGGCAGGAACTGTTTTCCTTGAATTATCATTCCATTCCTAGCTAACCATAAAACCCATAAAACCCATGCAACTGTACAGGGAAAGCCTTGTGATCTGTAACTGCTCTGTCCAAACACCAATTTAAGCAATCAGAGATAGATTCTTCTTCCCATTCCCCTTGACATTAAT
TAGTTTTAGACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTT
CCATATTACCTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTT
CTTTCCTGATCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCA
ATTCCATGTGCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGG
GGTTTACAGAAAAATGGGATCAATTCCACAAGAGGAAGTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGTGACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGC
CAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTACAAATTTCAAGAATATCAGCCTTCCAGA
TTTCTTCTAAGCCTAACATTTTGTAATAAGATTAGATCATATGGGTGTTTTCCTTAAACTAGCTTTACTTCTGGAAAATAATTCCTGAAGTGGACATGCTATGTATGTACTATGAATCCTTACAGGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTGCA
AAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGC
AAGAATGCAGGAA

>TRINITY_DN126351_c2_g1_i8 from sample A1 / Example unspliced isoform:

ATGCATACCTTACCTGATGACTTACCTGAATTGGCAGGAACTGTTTTCCTTGAATTATCATTCCATTCCTAGCTAACCATAAAACCCATAAAACCCATGCAACTGTACAGGGAAAGCCTTGTGATCTGTAACTGCTCTGTCCAAACACCAATTTAAGCAATCAGAGATAGATTCTTCTTCCCATTCCCCTTGACATTAAT
TAGTTTTAGACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTT
CCATATTACCTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTT
CTTTCCTGATCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCA
ATTCCATGTGCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGG
Ggtgagtgtaattcttctgtcaagttggtcatatatttgttaatgtcaagttggttgttgaaaattcataagctgcttgtgcgaacctcccaagccaccatgagaacatggttgtctaatcagcatggagttacatttatgcctttagcttctcctggccaaaatatgttgtatagtgaatgaactgagaagccatgtta
acccctcttcaattgtcagGTTTACAGAAAAATGGGATCAATTCCACAAGAGGAAGTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGTGACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTAC
AGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAG
AAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTGCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCA
AATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAAT
AAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTC
AAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTA
TCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGA
TGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACAC
TGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAA
ATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAA
ATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAAAAGTTTCTCAGCGCGAATGAACAATTTCATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGG
CACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGC
CTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATC
TGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGT
CATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCC
TCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGC

Intron 12 GTAAGATGTC ... ATTTGGTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	60.68	4	9	2
A2	60.72	5	5	10
A3	46.67	2.3	1	3
A4	68.35	1.7	5	2
A5	75	1	3	3
A6	81.82	1	5	0
A7	60.72	3	6	3
A8	60.38	2.3	3	4
A9	48.57	1.7	3	0
A10	52.19	2.3	3	2

>TRINITY_DN126351_c2_g1_i8 from sample A1 / Example spliced isoform

ATGCATACCTTACCTGATGACTTACCTGAATTGGCAGGAACTGTTTTCCTTGAATTATCATTCCATTCCTAGCTAACCATAAAACCCATAAAACCCATGCAACTGTACAGGGAAAGCCTTGTGATCTGTAACTGCTCTGTCCAAACACCAATTTAAGCAATCAGAGATAGATTCTTCTTCCCATTCCCCTTGACATTAAT
TAGTTTTAGACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTT
CCATATTACCTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTT
CTTTCCTGATCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCA
ATTCCATGTGCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGG
GGTGAGTGTAATTCTTCTGTCAAGTTGGTCATATATTTGTTAATGTCAAGTTGGTTGTTGAAAATTCATAAGCTGCTTGTGCGAACCTCCCAAGCCACCATGAGAACATGGTTGTCTAATCAGCATGGAGTTACATTTATGCCTTTAGCTTCTCCTGGCCAAAATATGTTGTATAGTGAATGAACTGAGAAGCCATGTTA
ACCCCTCTTCAATTGTCAGGTTTACAGAAAAATGGGATCAATTCCACAAGAGGAAGTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGTGACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTAC
AGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAG
AAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTGCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCA
AATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACATTTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAAT
AAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGTGGAAATGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTC
AAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCTGCAACCACATTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTA
TCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGTCTTCCAAAAATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGA
TGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAGATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACAC
TGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGATCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAA
ATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCTTAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAA
ATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAAAAGTTTCTCAGCGCGAATGAACAATTTCATGAAGCAGAACTTCAAATGTCTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGG
CACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGTAGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGC
CTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGAACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATC
TGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAAATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGT
CATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACTTCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCC
TCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTCTTGAGATCGCTCCTTCACGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGC

>TRINITY_DN126351_c2_g1_i3 from sample A1 / Example unspliced isoform:

ATGCATACCTTACCTGATGACTTACCTGAATTGGCAGGAACTGTTTTCCTTGAATTATCATTCCATTCCTAGCTAACCATAAAACCCATAAAACCCATGCAACTGTACAGGGAAAGCCTTGTGATCTGTAACTGCTCTGTCCAAACACCAATTTAAGCAATCAGAGATAGATTCTTCTTCCCATTCCCCTTGACATTAAT
TAGTTTTAGACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTT
CCATATTACCTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTT
CTTTCCTGATCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCA
ATTCCATGTGCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGG
GGTGAGTGTAATTCTTCTGTCAAGTTGGTCATATATTTGTTAATGTCAAGTTGGTTGTTGAAAATTCATAAGCTGCTTGTGCGAACCTCCCAAGCCACCATGAGAACATGGTTGTCTAATCAGCATGGAGTTACATTTATGCCTTTAGCTTCTCCTGGCCAAAATATGTTGTATAGTGAATGAACTGAGAAGCCATGTTA
ACCCCTCTTCAATTGTCAGGTTTACAGAAAAATGGGATCAATTCCACAAGAGGAAGgtaagatgtctccagttttaggaaactttgaagtttcaatacagaaaaaaaaatctttctagcacaggcagagaagaaacaatcttctatataaatatatattgtatttgcatagctggtacagctctatatagaactgtacag
attttatgtactctgttttgaataatgtctcatagatcctgtttgggtcttccaaggacaataataaaaaaatcattaattcatatgcattttttctctatccttgctgctcacatttttattttttttcttaatttgggcagTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGT
GACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGC
AAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTGCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTA
AATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACAT
TTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGTGGAAA
TGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCTGCAACCACA
TTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGTCTTCCAAAA
ATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAG
ATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGA
TCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCT
TAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAAAAGTTTCTCAGCGCGAATGAACAATTTCATGAAGCAGAACTTCAAATGT
CTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGT
AGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGA
ACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAA
ATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACT
TCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTCTTGAGATCGCTCCTTCA
CGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGC

Intron 13 GTATGCCTGC ... CAAATGGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	43.92	9	9	5
A2	60.56	7.5	16	7
A3	9.13	15	3	0
A4	0	5	0	0
A5	34.28	8	6	2
A6	14.29	3	1	0
A7	0	4	0	0
A8	0	1	0	0
A9	20.2	8	3	1
A10	100	0	1	1

>TRINITY_DN44062_c1_g2_i6 from sample A9 / Example spliced isoform

GTTTCCCGCCATGGAAATACCAAACTTATGAAATCACTGCAGAGAGTTGCAACACAAGCCTCTGAGTTTTTATCAAAAATGAGTTCCAGAACAGAAGAAGAAGGAGAGGAAGCTCTTCCGCTTCAGCCGCTGCTCATACACTCAATATCAGTGCGTGCCTTCAAATCCTTCGAACGGAAGCTCAAGATATCTCCTCTGAC
GTCCTTCGCATGCATTGTCGGTCCCAACGGCACCGGCAAGAGCGTCATCGGCGAAGCCCTGGCATTTGCACTGGGGGCATCGCCCAAAGTCCTAAGGGTCGATGCATTTTCTTCGCTCGTCAATCATCGTTCGGCTTCGGCTTCATCTTCTGCCAAGGTCATTCTCGTCTGAATTCATCTTTTCTTTTCTTCCCTTTGTT
AAGAAATATATAGGTGAATACACAGTTCAAGGGCAACTGCAGGTGAGTGTAGGGTTCGAACGAAGGGATGGCGGTGAGAAGGTGACGATCTATAGGGTTTTGTCCGGGTCCTCTACTAAATTCTACTGGAAAGATGATAATCAAACCCCGAAGAAGGAAATTTCCTTATCCGAGTTGAAACAGAAGCTAGCTAGTTTCAG
TATCCCCGCTAATAATCTAGATAGGTGATACTTTTTCATTTTTTTCTTGATTATTATTTTTATTTGAGCATTACAATTAAGCTAAATTTTAATTACTAATTTTGAAACGAACAACGACAAATATATATAGTTGTAATTTCTAAATATTTTTAAATTTCTACGAACTTTATCTAATATTTTTGAAATTTTTAGCTATTTTT
AAAGTAAGATCATTCTTTCTTATTTAATTGCGAAAACTTGTCGCTACAATATTTTCGCACAAATAAATCTGGTCGTGTTGCTTTCTCCATAATTTTTAGATAATCATATTTCTTTTGTCCACGAACAAAATCTGTATGTTGGTTATTTCAATTAGAATTCGAAATATACAAGCACTGTGATCCGGCTCTGTGATCCGGCT
CTGTGATCCAGCTGACACATGCCACTCTTTTTTTGTAATGTTGCAACTATATATTAAAAAAGAGAACCGAAGATTACATATCTGTTTACAAGCTTAGGTGGTTTGACGTGGGGAAACCACCACCCTACGCGCTCAAAAATGCTAGAGAAACTATTATTGTTACAAAAAAAACCTGTGCTAGGAGACCAGGTCTTCAAAAA
TGCTAGAGAAACTATTATTGTTACAAAAAAAACCTGTGCTAGGAGACCAGGTCTTCTAAGAGTCCTGACATAACGGACTTTGGAACAAACCAAACCAAAAAAACAGACTATGAAGCCAATGTAAACAAAAACACTGAAAATCACAGCAAGAACTTGGAACCACCAAAGCCAACCTATGAGCTTGCTCCTGTATGAGGAGG
ATTCGGTTTCTCTTCCAAAATTGGGCAGCTGCCAAAGAAGTCGTCGTCCCAGCCTTGAGGAGGGAGCTTAGGAGACAAAGGCTCCGCTTTGCGACGGGGGAGACGCTACCATCGTCAGATTTTCGGACTCTCTTGTATTGCAGGGGCCCGATGGTGGACGGCACAGGGAAGGCAGCCAGGAAGGAAGGGTCATCCGGATT
GGCCGTGGCCTCCGACGGTTGCCTTCAGTGACCACAGTGTCTTTGATAGATGGTTCAGCACCAGCGGCGGCCGAGACAGCACCAGATCT

>TRINITY_DN44062_c1_g2_i2 from sample A9 / Example unspliced isoform:

GTCATTCTCGTCTGAATTCATCTTTTCTTTTCTTCCCTTTGTTAAGAAATATATAGGTGAATACACAGTTCAAGGGCAACTGCAGGTGAGTGTAGGGTTCGAACGAAGGGATGGCGGTGAGAAGGTGACGATCTATAGGGTTTTGTCCGGGTCCTCTACTAAATTCTACTGGAAAGATGATAATCAAACCCCGAAGAAgt
atgcctgctcaaattaattcaaatcttactgtttacctatttcttctccgtcttcgtgtctaattagcattttcaaatggcagGGAAATTTCCTTATCCGAGTTGAAACAGAAGCTAGCTAGTTTCAGTATCCCCGCTAATAATCTAGATAGGT

Intron 14 GTACAAATTT ... ATCCTTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	55.56	6	9	6
A2	46.67	8	7	7
A3	48.72	10	13	6
A4	44.44	5	4	4
A5	60	3	6	3
A6	100	0	0	1
A7	42.86	2	2	1
A8	50	2	1	3
A9	20	6	3	0
A10	42.86	2	1	2

>TRINITY_DN126351_c2_g1_i3 from sample A1 / Example spliced isoform

ATGCATACCTTACCTGATGACTTACCTGAATTGGCAGGAACTGTTTTCCTTGAATTATCATTCCATTCCTAGCTAACCATAAAACCCATAAAACCCATGCAACTGTACAGGGAAAGCCTTGTGATCTGTAACTGCTCTGTCCAAACACCAATTTAAGCAATCAGAGATAGATTCTTCTTCCCATTCCCCTTGACATTAAT
TAGTTTTAGACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTT
CCATATTACCTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTT
CTTTCCTGATCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCA
ATTCCATGTGCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGG
GGTGAGTGTAATTCTTCTGTCAAGTTGGTCATATATTTGTTAATGTCAAGTTGGTTGTTGAAAATTCATAAGCTGCTTGTGCGAACCTCCCAAGCCACCATGAGAACATGGTTGTCTAATCAGCATGGAGTTACATTTATGCCTTTAGCTTCTCCTGGCCAAAATATGTTGTATAGTGAATGAACTGAGAAGCCATGTTA
ACCCCTCTTCAATTGTCAGGTTTACAGAAAAATGGGATCAATTCCACAAGAGGAAGGTAAGATGTCTCCAGTTTTAGGAAACTTTGAAGTTTCAATACAGAAAAAAAAATCTTTCTAGCACAGGCAGAGAAGAAACAATCTTCTATATAAATATATATTGTATTTGCATAGCTGGTACAGCTCTATATAGAACTGTACAG
ATTTTATGTACTCTGTTTTGAATAATGTCTCATAGATCCTGTTTGGGTCTTCCAAGGACAATAATAAAAAAATCATTAATTCATATGCATTTTTTCTCTATCCTTGCTGCTCACATTTTTATTTTTTTTCTTAATTTGGGCAGTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGT
GACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGCCAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGC
AAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTGCAAAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTA
AATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGCAAGAATGCAGGAACGACTAAACATCTCAAATGAGAGGAGGAGAGACCACAT
TTCACGAGCTGCACAGTTAACATCGGAGATTCATATCTCAAAGAAGGGTCTGGAGGAAAGTCATAAGTTTGAAGAGGATCACGAAATAAAAGTTTCAGCCACAAGAACTAGATTGTCTCAACTGCAGAGAGAAATTGACTTGATAAGTGATCAGAAGCTACCTAGGCTGAGAGAAGAGATTAGTAAGAATGAGGTGGAAA
TGAAACATTTGCTAAAGAAGCGACAAGATATTGAGAACAGACCAGATAAGTTATCTCGAGAGGATGAGGCAGCAAATGTTCTCATTCAAACATTAAAAGGAAAGTTGTGTGGGAGGATTACAGATTTGGCTACAGTTAGTGGCCACTTGGCAAAAGCAGTAAATTCCATTCTTTGTCATCTTACAAATCCTGCAACCACA
TTTGTAGTTGATGACAGAGATACAGCAAATATAATTATCTCATATTTTCAAGAAAAACGCATTGGCATTGCAACATGCGAGATTTTATCTGAGTTAAGTCTACAATTCAGGTGCAGAAATACTTTTGAAACTGGACCATATGTTAGACCAGTTTTGCAAGACCTCCAGTGTTCAGAAAATTATCGACCTGTCTTCCAAAA
ATATTTTGGAAATTGGTGTGTAGCAAAAGATCTTTATGCTGCAACCACATATTTCAAAAGGAAGCAAGGTTATTCTGAGACATATGATGTTGTGACTGAAGATGGAGTTATCTTCAAAAAGGATGGGGAAGTAATTGCTGCTAACTGGGACACAAAAGGGAAGGCAGCATTTAAATCTAGTGATGATATCTTCAAGCAAG
ATGAATCAAGAACCATTGTGATATTGGAGGAGACCCTAAAAGGGAAGGATAAACAGAAATATAAGTTAGAAGCAAGTCTAGCGACACTGCTAACTAATTTGAAGCTCATAAAATCTCAAAAACAAGATGCCTATGAACAAATGCAGAAACTAAGAGAAAGTGAAAAATATCATTTGGTTTCTAATACAGCAGCTATCAGA
TCTAAGCTTGAAGAACAGCAGATTGAGCTCGATACTATTCACAAAGTAATTGAAGATGATCGAGATGATCAGAAACTTCAAAAGGAAATTGAAGAATTGAAACAGGAGCAAATGATTTTGAAAAGCAAATTGGGGGTAGCTGAAAATTTTCTTTCATACAATCCTGAACTTGTTGAATTGAATGAGAGAATTAAACAGCT
TAATGAAGCAATGAGATCATACACAATCGAGATCCAACAGAAAAGATCATCTTTCAAGATGCTAAAAAATCAGTTGGAAACAGTAAAATCTGATGGTAAGTATAAGTCATCACTCTCAGAAAAATTAACAGCCCTTGCGACACACAAAGAAAAGTTTCTCAGCGCGAATGAACAATTTCATGAAGCAGAACTTCAAATGT
CTACCAGGAAAACAGAAATTGAGAAAATGAAAGCAAAAGTGATTGAATTTGAAACAAAGATTTCTGAGTGTAACAAAGAAGAGAAGGCACTAAGGTCAAGAGAGGTTTTTATAAAGGATGAGTTAGATGGGTTGGTGGCATCTGAAACAATAACAAAGGAACAATTGAGAAAGGTTCTTTTGGCGCTGCAAGACAGTTGT
AGACCTCAGCTCCACAAAAAGGTATGCCATGAACTGTCTAATCCGTCTTTTGAAGCACTTGCAAATGAAGCAGAAGATGAGGAAGGCCTGATCTTGGCTCAGGAGGAGATGTCTCTGAATGAAATCAGAAGGAACATTCGTGCCGATGCTTTAGAGGAGGATGTAAAGTACCGAAAGAATGAATCCTACTTTTTGATAGA
ACTTGATAAACTTATTGAAATGATAGAATCACAAAGAAATCACAAGGACAAGCTAGAAAATGAGAGGTTTAATATCTTTACAAAATCTGTCAAAAAGCTGAATCGCGTGCTGTCAAAAACATATCAAAATCTTACACAACATGGAGATGCATATCTCTCTTTTACAGAGGAAAAGAGTCTCCTTTTTTCCGATGGAGTAA
ATCTACAAGTGCGCCCAGATCGTCATAAGTGGCGTAATTTCAATTCCCTGTCCGGGGGACAACAAGCTCTAGCGTCTTTAGCCTTGTCATTCAGTTTACAAGCAATGTTTCCTTCACCTTTCTACTTCTTTGATGAGATTGATGCTTCCCTGGATACAAAAAATGCACGGCTAGTTGCAGAATACATCAAGAATCAAACT
TCTGCTCAGTATATTGTGGTTTCACATCGGCCTCAGTTATATGATCTTGCAACATCTTTGGTGGGGGTCTATCATTACAATGGTTCCTCGACATGTATAACTGTCAAAGTCTAAGAATCAAGATCATATTGTACATACGAGGCATTAGTTTGATATTCACATACCTCAGAATGATGGAACCTCTTGAGATCGCTCCTTCA
CGTCTGGAAAGCCAGACCGATAGAATGTCGATTGTGATAGCAGCATGTGCACATTTATGAAAAGTAGC

>TRINITY_DN126351_c2_g1_i1 from sample A1 / Example unspliced isoform:

ATGCATACCTTACCTGATGACTTACCTGAATTGGCAGGAACTGTTTTCCTTGAATTATCATTCCATTCCTAGCTAACCATAAAACCCATAAAACCCATGCAACTGTACAGGGAAAGCCTTGTGATCTGTAACTGCTCTGTCCAAACACCAATTTAAGCAATCAGAGATAGATTCTTCTTCCCATTCCCCTTGACATTAAT
TAGTTTTAGACTCCCTCCCACACTTCTTTTGCGAATTGACAGTGCACTAATAGATGGTCCACCGACTCCTCATTAATCCTATAGAACAGACACCTCTCTGGACCTTCCCAAGGCCTTTTTCTACAATTATCCCAACTTAACACTTTGTTTGCTAGTACAAGCCATAAGAATATTTTAGTTTTCAGAGGACAACTCAGCTT
CCATATTACCTTCCACCACCATTTCCTTTCACCTTCCTCACTCTCAACTGCCTTTGCTGCATAACCCAATTTAGCTGTGTACATTCCTGAAGCTTTATTCTCTGAACAACCAAACCCCTATTTTTATTTTAACCAACCAGTGGATAGGCTTTAACTAATGCCTTCCATGCCACAGATGCCCCCTCGAAAGTCCTTTCTTT
CTTTCCTGATCCAATCCTCTACAGACCCTGGGGCTATATATTTAGCTTGCACTACCTTACCTCTTAGATAATCATACTTATGTGTCCCATCTTATTCTATTTTGCAGGTTTATAGTGATGCAGAACCGAGTTTCTGCTAAAATAAAACAACCACAAGAGTTGATCAAGGTATCTGATCTTAAAACTGTGCTTAATTTGCA
ATTCCATGTGCTATGTCTAAATATTCAGGGTTAGCAGCATCTGGAACGTGTAATCGGAACTGGCCACTATGAAGAGGAGATTAAAGAAGCAGACCAGAAGATTGGCAAACAAATCACTGAGCTGGAATGTGTGCAGCAAAGCTTGTCGGAGATTGAATTGAAGAGAAAACAACTCAGCCCTGAAGTTGAAAAATGGAAGG
GGTTTACAGAAAAATGGGATCAATTCCACAAGAGGAAGTCACTATTTCTCAGACGCCAAGAGAAATCCCTGCATGCAAATTTGCAAATATATAGTGACCAGAAGAAAGAGAAAGAACATGAATTCCTTCAAATTCAAAACAGCATCAATGTATCTACAACTTTCTCTGCCTTTGCTCATTACAGATTGAATTTACTGAGC
CAAATTGTTGTCTTTCTTAAACATGTTTTATTAGACTTTACAAGGGTCATTAACAAATTTGAATCTGGAGCACACTGAATTGCATACTCTCCTGCAAGAGTGTCAAAGCAAACATAAAATTGCAAAAAAACAATATGATTCGCAAAGGATTAAAATGATCAAAGAAGAGgtacaaatttcaagaatatcagccttccaga
tttcttctaagcctaacattttgtaataagattagatcatatgggtgttttccttaaactagctttacttctggaaaataattcctgaagtggacatgctatgtatgtactatgaatccttacagGTGCAGTTGAAAGAAGCTGAAAAGGATCTTGCTCTGCAGAAAGACCGTCATCACAAGGAACAAAAATCTCTTGCA
AAATGTGAAAAAGAAGCCGAGGAAAAAATGAATTTGCTTTCTCTGGATGTAAATAAGCTTGAAAGCAAGAAACAAGTGATTTGCAAGGAAAAGGAAGAGACTGAGCAAAAACGAGTGTTAATTTTAAGTTCAGGGTCAAATAACTTGAAACTGGATGATTCTACTGTCCAAGAGGAAGCTTTCCTTACCATGAAGATTGC
AAGAATGCAGGAA