NA ----> NA

Intron 1 GCATGTCATC ... GGTTTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	69.39	15	24	44
A2	75.38	8	21	28
A3	74.42	11	24	40
A4	83.78	6	27	35
A5	77.14	4	16	11
A6	58.14	9	5	20
A7	69.64	34	79	77
A8	77.53	10	36	33
A9	73.74	26	62	84
A10	79.06	20	83	68

>TRINITY_DN112329_c0_g1_i3 from sample A3 / Example spliced isoform

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGTGAGCGAAAAGATTCGACGAACGAGGAAGTTGAGGTTTAACGGCGATTTCGTGGAGAATAATTGCGGGG
ATTCCAGACCACGAAGCATTTTGCAGTGTTTTGATTTTATGAAATCGATGTTCGTGCTGGTGTTTGAATGGCGCTTGTGAGGGTTTAACTTTACACTTACAGTTTGCCATTGCCGTGATTTTCTGCAAATGCAGAGATTAGCAAACGGCAAATATTCTTTGTTGCCTATTCCGCGTCTGCAATCGCTTTAAAGATCTTGC
AGGAAAATGCAAGTGGTGGATAGCCGTTCTACAGGGCAAAGCCCCTCTGCGTCAAGTAGTTCGTCATCCAAGAAGGAGAAGAAGAAGCAGGCTAAGGAAGAAAGAGACAGACAAAAGCAAGCCGAGAAGAAGAAACGGCGGCTTGAAAAGGCTCTCGCAACGGCTACGGCGATTCGGATAGAACTTGAACAAAAGAAGCA
GAAGAGAAAGGAAGAAGAGCAAAGATTGGATGAAGAAGGAGCAGCTTTGGCTGAGGCTGTTGCTCTACAAGTACTGGTAGAAGAAGATATAGGAATTCAAACTTCGGCTTCAAATTTCACTGAGCTTGAAAATATTTGTGATCACGAATCCTTTTCAAGTGTAACAAGGAAAGAAGTCGGGCAGCAAATTGTAGTAAAGG
AACGGGACAGTAATGGGAGACATGTAAGGATATTGGACACCAGGGAAATTGATGATCAGTCCTGGATCAATGTTAGAGTCTTAGAAGGGAGATCAGATTTCAGAAATGAAGAATTATACCGAGGGGAGGATGGTTCGTGCCATGCAGGTGAAAGCAGTAGCAGCATAGAGGAAGAATTCAGATTAACTAGTGAAAGGGCA
AGGGATGCTGAAGTAGCTGCTGGATTGGCTGCAGCACGTGCTGTGGCTGCACTACGGATTGCTGAAGAAGCAAGAGCCGAGGCAGAGGCTGCTAGAATAGCAGCAGAGTTGTCCATGGTCAAGAATTTGGAGAAGCGAAACTGTTCTCACACGGAACGGATTTTGCATGAGTCTATATTGCGACCAAAGAGTGCAGAAGA
GGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAGCATGCACTTCAAGAAAAGACCAAAAAGGTTCTTCAGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATCAAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCA
CAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGTCTAATGGCCATGATATGGAATATGATACAGCTTTGTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGATAACGGACATTAGTTTTTCTTGGTGGC

>TRINITY_DN112329_c0_g1_i1 from sample A3 / Example unspliced isoform:

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGgcatgtcatcaccaccttaaacttttcattaaatttaattaaacgatttcaagagcgaatgacatccga
tctcttgttctggcggccgaaatggtcccaaattccaatatctctcggataaccttacaatttcttggatctccaaaagattttagcaaattcctttaattttcaaatcacatcctgtctcggtgcgaagaactcgatacatttcggtaccttgcgatgcaaattacggcttatgttttatgcttcgattaggtttctgt
tgattctttaaccgtcggatctgaatcacctgcaagtgtttggagacatttcaattctgttcgtagaaatgatgatcgcagccagtaaatttcgtgttcctgtgcctctgcaacagcctttcgttctcgaaattactatctttttgccttacaggagtaatatttcacctttgtcgtgctaacttttgtggaagcagcgg
ctcatggtcgtaaattcgatgtaacagttcaatgacaagaggatttaggtttttcagTGAGCGAAAAGATTCGACGAACGAGGAAGTTGAGGTTTAACGGCGATTTCGTGGAGAATAATTGCGGGGATTCCAGACCACGAAGCATTTTGCAGTGTTTTGATTTTATGAAATCGATGTTCGTGCTGGTGTTTGAATGGCGC
TTGTGAGGGTTTAACTTTACACTTACAGTTTGCCATTGCCGTGATTTTCTGCAAATGCAGAGATTAGCAAACGGCAAATATTCTTTGTTGCCTATTCCGCGTCTGCAATCGCTTTAAAGATCTTGCAGGAAAATGCAAGTGGTGGATAGCCGTTCTACAGGGCAAAGCCCCTCTGCGTCAAGTAGTTCGTCATCCAAGAA
GGAGAAGAAGAAGCAGGCTAAGGAAGAAAGAGACAGACAAAAGCAAGCCGAGAAGAAGAAACGGCGGCTTGAAAAGGCTCTCGCAACGGCTACGGCGATTCGGATAGAACTTGAACAAAAGAAGCAGAAGAGAAAGGAAGAAGAGCAAAGATTGGATGAAGAAGGAGCAGCTTTGGCTGAGGCTGTTGCTCTACAAGTAC
TGGTAGAAGAAGATATAGGAATTCAAACTTCGGCTTCAAATTTCACTGAGCTTGAAAATATTTGTGATCACGAATCCTTTTCAAGTGTAACAAGGAAAGAAGTCGGGCAGCAAATTGTAGTAAAGGAACGGGACAGTAATGGGAGACATGTAAGGATATTGGACACCAGGGAAATTGATGATCAGTCCTGGATCAATGTT
AGAGTCTTAGAAGGGAGATCAGATTTCAGAAATGAAGAATTATACCGAGGGGAGGATGGTTCGTGCCATGCAGGTGAAAGCAGTAGCAGCATAGAGGAAGAATTCAGATTAACTAGTGAAAGGGCAAGGGATGCTGAAGTAGCTGCTGGATTGGCTGCAGCACGTGCTGTGGCTGCACTACGGATTGCTGAAGAAGCAAG
AGCCGAGGCAGAGGCTGCTAGAATAGCAGCAGAGTTGTCCATGGTCAAGAATTTGGAGAAGCGAAACTGTTCTCACACGGAACGGATTTTGCATGAGTCTATATTGCGACCAAAGAGTGCAGAAGAGGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAGCATGCACTTCAAGAAAAGACCAAAAAGGTTCTTC
AGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATCAAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCACAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGTCTAATGGCCATGATATGGAATATGATACAGCTTT
GTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGATAACGGACATTAGTTTTTCTTGGTGGC

Intron 2 GCATGTCATC ... CTTCGATTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	82.05	7	24	40
A2	70.15	10	21	26
A3	77.78	7	24	25
A4	68.09	15	27	37
A5	75	6	16	20
A6	51.02	12	5	20
A7	75	27	79	83
A8	70.3	15	36	35
A9	75.34	27	62	103
A10	87.3	11.9	83	81

>TRINITY_DN112329_c0_g1_i4 from sample A3 / Example spliced isoform

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGGTTTCTGTTGATTCTTTAACCGTCGGATCTGAATCACCTGCAAGTGTTTGGAGACATTTCAATTCTGTT
CGTAGAAATGATGATCGCAGCCAGTAAATTTCGTGTTCCTGTGCCTCTGCAACAGCCTTTCGTTCTCGAAATTACTATCTTTTTGCCTTACAGGAGTAATATTTCACCTTTGTCGTGCTAACTTTTGTGGAAGCAGCGGCTCATGGTCGTAAATTCGATGTAACAGTTCAATGACAAGAGGATTTAGGTTTTTCAGTGAG
CGAAAAGATTCGACGAACGAGGAAGTTGAGGTTTAACGGCGATTTCGTGGAGAATAATTGCGGGGATTCCAGACCACGAAGCATTTTGCAGTGTTTTGATTTTATGAAATCGATGTTCGTGCTGGTGTTTGAATGGCGCTTGTGAGGGTTTAACTTTACACTTACAGTTTGCCATTGCCGTGATTTTCTGCAAATGCAGA
GATTAGCAAACGGCAAATATTCTTTGTTGCCTATTCCGCGTCTGCAATCGCTTTAAAGATCTTGCAGGAAAATGCAAGTGGTGGATAGCCGTTCTACAGGGCAAAGCCCCTCTGCGTCAAGTAGTTCGTCATCCAAGAAGGAGAAGAAGAAGCAGGCTAAGGAAGAAAGAGACAGACAAAAGCAAGCCGAGAAGAAGAAA
CGGCGGCTTGAAAAGGCTCTCGCAACGGCTACGGCGATTCGGATAGAACTTGAACAAAAGAAGCAGAAGAGAAAGGAAGAAGAGCAAAGATTGGATGAAGAAGGAGCAGCTTTGGCTGAGGCTGTTGCTCTACAAGTACTGGTAGAAGAAGATATAGGAATTCAAACTTCGGCTTCAAATTTCACTGAGCTTGAAAATAT
TTGTGATCACGAATCCTTTTCAAGTGTAACAAGGAAAGAAGTCGGGCAGCAAATTGTAGTAAAGGAACGGGACAGTAATGGGAGACATGTAAGGATATTGGACACCAGGGAAATTGATGATCAGTCCTGGATCAATGTTAGAGTCTTAGAAGGGAGATCAGATTTCAGAAATGAAGAATTATACCGAGGGGAGGATGGTT
CGTGCCATGCAGGTGAAAGCAGTAGCAGCATAGAGGAAGAATTCAGATTAACTAGTGAAAGGGCAAGGGATGCTGAAGTAGCTGCTGGATTGGCTGCAGCACGTGCTGTGGCTGCACTACGGATTGCTGAAGAAGCAAGAGCCGAGGCAGAGGCTGCTAGAATAGCAGCAGAGTTGTCCATGGTCAAGAATTTGGAGAAG
CGAAACTGTTCTCACACGGAACGGATTTTGCATGAGTCTATATTGCGACCAAAGAGTGCAGAAGAGGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAGCATGCACTTCAAGAAAAGACCAAAAAGGTTCTTCAGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATC
AAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCACAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGTCTAATGGCCATGATATGGAATATGATACAGCTTTGTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGA
TAACGGACATTAGTTTTTCTTGGTGGC

>TRINITY_DN112329_c0_g1_i1 from sample A3 / Example unspliced isoform:

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGgcatgtcatcaccaccttaaacttttcattaaatttaattaaacgatttcaagagcgaatgacatccga
tctcttgttctggcggccgaaatggtcccaaattccaatatctctcggataaccttacaatttcttggatctccaaaagattttagcaaattcctttaattttcaaatcacatcctgtctcggtgcgaagaactcgatacatttcggtaccttgcgatgcaaattacggcttatgttttatgcttcgattagGTTTCTGT
TGATTCTTTAACCGTCGGATCTGAATCACCTGCAAGTGTTTGGAGACATTTCAATTCTGTTCGTAGAAATGATGATCGCAGCCAGTAAATTTCGTGTTCCTGTGCCTCTGCAACAGCCTTTCGTTCTCGAAATTACTATCTTTTTGCCTTACAGGAGTAATATTTCACCTTTGTCGTGCTAACTTTTGTGGAAGCAGCGG
CTCATGGTCGTAAATTCGATGTAACAGTTCAATGACAAGAGGATTTAGGTTTTTCAGTGAGCGAAAAGATTCGACGAACGAGGAAGTTGAGGTTTAACGGCGATTTCGTGGAGAATAATTGCGGGGATTCCAGACCACGAAGCATTTTGCAGTGTTTTGATTTTATGAAATCGATGTTCGTGCTGGTGTTTGAATGGCGC
TTGTGAGGGTTTAACTTTACACTTACAGTTTGCCATTGCCGTGATTTTCTGCAAATGCAGAGATTAGCAAACGGCAAATATTCTTTGTTGCCTATTCCGCGTCTGCAATCGCTTTAAAGATCTTGCAGGAAAATGCAAGTGGTGGATAGCCGTTCTACAGGGCAAAGCCCCTCTGCGTCAAGTAGTTCGTCATCCAAGAA
GGAGAAGAAGAAGCAGGCTAAGGAAGAAAGAGACAGACAAAAGCAAGCCGAGAAGAAGAAACGGCGGCTTGAAAAGGCTCTCGCAACGGCTACGGCGATTCGGATAGAACTTGAACAAAAGAAGCAGAAGAGAAAGGAAGAAGAGCAAAGATTGGATGAAGAAGGAGCAGCTTTGGCTGAGGCTGTTGCTCTACAAGTAC
TGGTAGAAGAAGATATAGGAATTCAAACTTCGGCTTCAAATTTCACTGAGCTTGAAAATATTTGTGATCACGAATCCTTTTCAAGTGTAACAAGGAAAGAAGTCGGGCAGCAAATTGTAGTAAAGGAACGGGACAGTAATGGGAGACATGTAAGGATATTGGACACCAGGGAAATTGATGATCAGTCCTGGATCAATGTT
AGAGTCTTAGAAGGGAGATCAGATTTCAGAAATGAAGAATTATACCGAGGGGAGGATGGTTCGTGCCATGCAGGTGAAAGCAGTAGCAGCATAGAGGAAGAATTCAGATTAACTAGTGAAAGGGCAAGGGATGCTGAAGTAGCTGCTGGATTGGCTGCAGCACGTGCTGTGGCTGCACTACGGATTGCTGAAGAAGCAAG
AGCCGAGGCAGAGGCTGCTAGAATAGCAGCAGAGTTGTCCATGGTCAAGAATTTGGAGAAGCGAAACTGTTCTCACACGGAACGGATTTTGCATGAGTCTATATTGCGACCAAAGAGTGCAGAAGAGGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAGCATGCACTTCAAGAAAAGACCAAAAAGGTTCTTC
AGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATCAAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCACAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGTCTAATGGCCATGATATGGAATATGATACAGCTTT
GTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGATAACGGACATTAGTTTTTCTTGGTGGC

Intron 3 GCATGTCATC ... TTTGCATGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	91.11	4	24	41
A2	75	14	21	42
A3	80.33	12	24	49
A4	100	0	27	6
A5	100	0	16	12
A6	80.56	21	5	87
A7	78.62	62	79	228
A8	78.99	71	36	267
A9	81.03	55	62	235
A10	81.36	44	83	192

>TRINITY_DN112329_c0_g1_i5 from sample A3 / Example spliced isoform

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGTCTATATTGCGACCAAAGAGTGCAGAAGAGGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAG
CATGCACTTCAAGAAAAGACCAAAAAGGTTCTTCAGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATCAAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCACAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGT
CTAATGGCCATGATATGGAATATGATACAGCTTTGTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGATAACGGACATTAGTTTTTCTTGGTGGC

>TRINITY_DN112329_c0_g1_i1 from sample A3 / Example unspliced isoform:

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGgcatgtcatcaccaccttaaacttttcattaaatttaattaaacgatttcaagagcgaatgacatccga
tctcttgttctggcggccgaaatggtcccaaattccaatatctctcggataaccttacaatttcttggatctccaaaagattttagcaaattcctttaattttcaaatcacatcctgtctcggtgcgaagaactcgatacatttcggtaccttgcgatgcaaattacggcttatgttttatgcttcgattaggtttctgt
tgattctttaaccgtcggatctgaatcacctgcaagtgtttggagacatttcaattctgttcgtagaaatgatgatcgcagccagtaaatttcgtgttcctgtgcctctgcaacagcctttcgttctcgaaattactatctttttgccttacaggagtaatatttcacctttgtcgtgctaacttttgtggaagcagcgg
ctcatggtcgtaaattcgatgtaacagttcaatgacaagaggatttaggtttttcagtgagcgaaaagattcgacgaacgaggaagttgaggtttaacggcgatttcgtggagaataattgcggggattccagaccacgaagcattttgcagtgttttgattttatgaaatcgatgttcgtgctggtgtttgaatggcgc
ttgtgagggtttaactttacacttacagtttgccattgccgtgattttctgcaaatgcagagattagcaaacggcaaatattctttgttgcctattccgcgtctgcaatcgctttaaagatcttgcaggaaaatgcaagtggtggatagccgttctacagggcaaagcccctctgcgtcaagtagttcgtcatccaagaa
ggagaagaagaagcaggctaaggaagaaagagacagacaaaagcaagccgagaagaagaaacggcggcttgaaaaggctctcgcaacggctacggcgattcggatagaacttgaacaaaagaagcagaagagaaaggaagaagagcaaagattggatgaagaaggagcagctttggctgaggctgttgctctacaagtac
tggtagaagaagatataggaattcaaacttcggcttcaaatttcactgagcttgaaaatatttgtgatcacgaatccttttcaagtgtaacaaggaaagaagtcgggcagcaaattgtagtaaaggaacgggacagtaatgggagacatgtaaggatattggacaccagggaaattgatgatcagtcctggatcaatgtt
agagtcttagaagggagatcagatttcagaaatgaagaattataccgaggggaggatggttcgtgccatgcaggtgaaagcagtagcagcatagaggaagaattcagattaactagtgaaagggcaagggatgctgaagtagctgctggattggctgcagcacgtgctgtggctgcactacggattgctgaagaagcaag
agccgaggcagaggctgctagaatagcagcagagttgtccatggtcaagaatttggagaagcgaaactgttctcacacggaacggattttgcatgagTCTATATTGCGACCAAAGAGTGCAGAAGAGGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAGCATGCACTTCAAGAAAAGACCAAAAAGGTTCTTC
AGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATCAAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCACAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGTCTAATGGCCATGATATGGAATATGATACAGCTTT
GTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGATAACGGACATTAGTTTTTCTTGGTGGC

Intron 4 GTTTCTGTTG ... TTTGCATGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	91.11	4	7	41
A2	75	14	10	42
A3	80.33	12	7	49
A4	100	0	15	6
A5	100	0	6	12
A6	80.56	21	12	87
A7	78.62	62	27	228
A8	78.99	71	15	267
A9	81.03	55	27	235
A10	81.36	44	11.5	192

>TRINITY_DN112329_c0_g1_i5 from sample A3 / Example spliced isoform

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGTCTATATTGCGACCAAAGAGTGCAGAAGAGGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAG
CATGCACTTCAAGAAAAGACCAAAAAGGTTCTTCAGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATCAAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCACAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGT
CTAATGGCCATGATATGGAATATGATACAGCTTTGTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGATAACGGACATTAGTTTTTCTTGGTGGC

>TRINITY_DN112329_c0_g1_i4 from sample A3 / Example unspliced isoform:

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGgtttctgttgattctttaaccgtcggatctgaatcacctgcaagtgtttggagacatttcaattctgtt
cgtagaaatgatgatcgcagccagtaaatttcgtgttcctgtgcctctgcaacagcctttcgttctcgaaattactatctttttgccttacaggagtaatatttcacctttgtcgtgctaacttttgtggaagcagcggctcatggtcgtaaattcgatgtaacagttcaatgacaagaggatttaggtttttcagtgag
cgaaaagattcgacgaacgaggaagttgaggtttaacggcgatttcgtggagaataattgcggggattccagaccacgaagcattttgcagtgttttgattttatgaaatcgatgttcgtgctggtgtttgaatggcgcttgtgagggtttaactttacacttacagtttgccattgccgtgattttctgcaaatgcaga
gattagcaaacggcaaatattctttgttgcctattccgcgtctgcaatcgctttaaagatcttgcaggaaaatgcaagtggtggatagccgttctacagggcaaagcccctctgcgtcaagtagttcgtcatccaagaaggagaagaagaagcaggctaaggaagaaagagacagacaaaagcaagccgagaagaagaaa
cggcggcttgaaaaggctctcgcaacggctacggcgattcggatagaacttgaacaaaagaagcagaagagaaaggaagaagagcaaagattggatgaagaaggagcagctttggctgaggctgttgctctacaagtactggtagaagaagatataggaattcaaacttcggcttcaaatttcactgagcttgaaaatat
ttgtgatcacgaatccttttcaagtgtaacaaggaaagaagtcgggcagcaaattgtagtaaaggaacgggacagtaatgggagacatgtaaggatattggacaccagggaaattgatgatcagtcctggatcaatgttagagtcttagaagggagatcagatttcagaaatgaagaattataccgaggggaggatggtt
cgtgccatgcaggtgaaagcagtagcagcatagaggaagaattcagattaactagtgaaagggcaagggatgctgaagtagctgctggattggctgcagcacgtgctgtggctgcactacggattgctgaagaagcaagagccgaggcagaggctgctagaatagcagcagagttgtccatggtcaagaatttggagaag
cgaaactgttctcacacggaacggattttgcatgagTCTATATTGCGACCAAAGAGTGCAGAAGAGGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAGCATGCACTTCAAGAAAAGACCAAAAAGGTTCTTCAGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATC
AAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCACAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGTCTAATGGCCATGATATGGAATATGATACAGCTTTGTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGA
TAACGGACATTAGTTTTTCTTGGTGGC

Intron 5 GTTTCTGTTG ... GGTTTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	74.58	15	7	44
A2	77.78	8	10	28
A3	78.43	11	7	40
A4	85.37	6	15	35
A5	73.33	4	6	11
A6	68.97	9	12	20
A7	69.37	34	27	77
A8	76.74	10	15	33
A9	76.36	26	27	84
A10	77.27	20	11.7	68

>TRINITY_DN112329_c0_g1_i3 from sample A3 / Example spliced isoform

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGTGAGCGAAAAGATTCGACGAACGAGGAAGTTGAGGTTTAACGGCGATTTCGTGGAGAATAATTGCGGGG
ATTCCAGACCACGAAGCATTTTGCAGTGTTTTGATTTTATGAAATCGATGTTCGTGCTGGTGTTTGAATGGCGCTTGTGAGGGTTTAACTTTACACTTACAGTTTGCCATTGCCGTGATTTTCTGCAAATGCAGAGATTAGCAAACGGCAAATATTCTTTGTTGCCTATTCCGCGTCTGCAATCGCTTTAAAGATCTTGC
AGGAAAATGCAAGTGGTGGATAGCCGTTCTACAGGGCAAAGCCCCTCTGCGTCAAGTAGTTCGTCATCCAAGAAGGAGAAGAAGAAGCAGGCTAAGGAAGAAAGAGACAGACAAAAGCAAGCCGAGAAGAAGAAACGGCGGCTTGAAAAGGCTCTCGCAACGGCTACGGCGATTCGGATAGAACTTGAACAAAAGAAGCA
GAAGAGAAAGGAAGAAGAGCAAAGATTGGATGAAGAAGGAGCAGCTTTGGCTGAGGCTGTTGCTCTACAAGTACTGGTAGAAGAAGATATAGGAATTCAAACTTCGGCTTCAAATTTCACTGAGCTTGAAAATATTTGTGATCACGAATCCTTTTCAAGTGTAACAAGGAAAGAAGTCGGGCAGCAAATTGTAGTAAAGG
AACGGGACAGTAATGGGAGACATGTAAGGATATTGGACACCAGGGAAATTGATGATCAGTCCTGGATCAATGTTAGAGTCTTAGAAGGGAGATCAGATTTCAGAAATGAAGAATTATACCGAGGGGAGGATGGTTCGTGCCATGCAGGTGAAAGCAGTAGCAGCATAGAGGAAGAATTCAGATTAACTAGTGAAAGGGCA
AGGGATGCTGAAGTAGCTGCTGGATTGGCTGCAGCACGTGCTGTGGCTGCACTACGGATTGCTGAAGAAGCAAGAGCCGAGGCAGAGGCTGCTAGAATAGCAGCAGAGTTGTCCATGGTCAAGAATTTGGAGAAGCGAAACTGTTCTCACACGGAACGGATTTTGCATGAGTCTATATTGCGACCAAAGAGTGCAGAAGA
GGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAGCATGCACTTCAAGAAAAGACCAAAAAGGTTCTTCAGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATCAAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCA
CAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGTCTAATGGCCATGATATGGAATATGATACAGCTTTGTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGATAACGGACATTAGTTTTTCTTGGTGGC

>TRINITY_DN112329_c0_g1_i4 from sample A3 / Example unspliced isoform:

AACGGAATCATTAAATATCTTCGCATGGACATGTACAAGGCGGAGGAAACATCAGCATTAAATGTCACTGAATGGGAGCACTCAACTCCGAAGAGGAAACGCCAGCATGGTGGAGTAACAGAGAGAAACAGgtttctgttgattctttaaccgtcggatctgaatcacctgcaagtgtttggagacatttcaattctgtt
cgtagaaatgatgatcgcagccagtaaatttcgtgttcctgtgcctctgcaacagcctttcgttctcgaaattactatctttttgccttacaggagtaatatttcacctttgtcgtgctaacttttgtggaagcagcggctcatggtcgtaaattcgatgtaacagttcaatgacaagaggatttaggtttttcagTGAG
CGAAAAGATTCGACGAACGAGGAAGTTGAGGTTTAACGGCGATTTCGTGGAGAATAATTGCGGGGATTCCAGACCACGAAGCATTTTGCAGTGTTTTGATTTTATGAAATCGATGTTCGTGCTGGTGTTTGAATGGCGCTTGTGAGGGTTTAACTTTACACTTACAGTTTGCCATTGCCGTGATTTTCTGCAAATGCAGA
GATTAGCAAACGGCAAATATTCTTTGTTGCCTATTCCGCGTCTGCAATCGCTTTAAAGATCTTGCAGGAAAATGCAAGTGGTGGATAGCCGTTCTACAGGGCAAAGCCCCTCTGCGTCAAGTAGTTCGTCATCCAAGAAGGAGAAGAAGAAGCAGGCTAAGGAAGAAAGAGACAGACAAAAGCAAGCCGAGAAGAAGAAA
CGGCGGCTTGAAAAGGCTCTCGCAACGGCTACGGCGATTCGGATAGAACTTGAACAAAAGAAGCAGAAGAGAAAGGAAGAAGAGCAAAGATTGGATGAAGAAGGAGCAGCTTTGGCTGAGGCTGTTGCTCTACAAGTACTGGTAGAAGAAGATATAGGAATTCAAACTTCGGCTTCAAATTTCACTGAGCTTGAAAATAT
TTGTGATCACGAATCCTTTTCAAGTGTAACAAGGAAAGAAGTCGGGCAGCAAATTGTAGTAAAGGAACGGGACAGTAATGGGAGACATGTAAGGATATTGGACACCAGGGAAATTGATGATCAGTCCTGGATCAATGTTAGAGTCTTAGAAGGGAGATCAGATTTCAGAAATGAAGAATTATACCGAGGGGAGGATGGTT
CGTGCCATGCAGGTGAAAGCAGTAGCAGCATAGAGGAAGAATTCAGATTAACTAGTGAAAGGGCAAGGGATGCTGAAGTAGCTGCTGGATTGGCTGCAGCACGTGCTGTGGCTGCACTACGGATTGCTGAAGAAGCAAGAGCCGAGGCAGAGGCTGCTAGAATAGCAGCAGAGTTGTCCATGGTCAAGAATTTGGAGAAG
CGAAACTGTTCTCACACGGAACGGATTTTGCATGAGTCTATATTGCGACCAAAGAGTGCAGAAGAGGAAAGGAATGAGCTGAAGGCACAACTTCTACAGATGGAGCATGCACTTCAAGAAAAGACCAAAAAGGTTCTTCAGTTAGAGCAGCACTTGGAATATGTTAAGGAATATCTGACAGGATGCGAAGCTACGACATC
AAATTCAAATAATAATGATGCCTCCGAAGAGAGCATGAAGAGGGAATCAGAAATATCAAGTATCACAGCTACAAAATCATTTGGTGATTCTGTTGACTTTTAGGTCTAATGGCCATGATATGGAATATGATACAGCTTTGTTGCTGTTGATTCCTATGAAGTTTAGTCCTTTTGATACCAATATAACGTTTTTTATTTGA
TAACGGACATTAGTTTTTCTTGGTGGC