NA ----> NA

Intron 1 GTAAATCGAG ... TGTTTTATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	29.62	13	11	0
A2	63.64	2	6	1
A3	50	3	4	2
A4	34.73	4	3	1.3
A5	73.81	1	3	2.7
A6	53.82	25.7	35.7	24
A7	48.21	30.7	41	16
A8	52.94	16	29	7
A9	79.86	5	25	14.7
A10	43.9	17	15	11.7

>TRINITY_DN37466_c0_g1_i3 from sample A6 / Example spliced isoform

AAAGAAAAGAGGGAGAACCGTTAGGGTTTCTCAAGAAGAGAAAAGTAGTTATGTTGAAGTAAAAGGGAGGCCGAAGGCTCTCTCTCAAGAAAAAGGTGTGCGACTATACCTTTGCACCAAAAAAAGGAGATGGAGGCTAGTTTGATAAGGACAAATGAGAGGAACTCAACGCAAATCAAAGAAGGAAGGGCACATTTCTA
TACCGGGTTTTGGAGATGCTATTCAATTTTGCAGATTGAATGTAAAGGAACTTTATAATTGTTCCTGTATTCTGCCAGTGAAGAAAAGGGCGCAGCTCCTTTCGGAGCAAGCAACTCTTTCGGAGATATCCTGCTACAGAACATGGAATGTGCGGCCTCCTGGCAGGAGAGCCAGAGCCAGACCTCACTATTGGCTATCT
TTTTATATATTATATACATGTACTTATATGCCTCTAGATGAAAGCCGCCCATTCTCCTAGATTGATATCTTTCAGTGCCTCTCCTTTGAGTTTTTAGATATGGTTTTATAAATGTGTGGACTGCCGCTCATGTGGGGGCAAGTCGCCTTTTCTTTTGTTAAACTGCTTGTGGTTTTGACAAGAGCGTAGGGAGCGTCAAT
AACGGAGACTGCTCTTTATTTTTATATTTCTCTGTTGTTGATTATTGGCATTCTTCTTCTTGGATGAAGAAGAGAAGGGTAAAACCCTCCGCTAAAATTTATGTTTATATTTCTATATTAGATCTACAATAAATCAGCCTGAGCAAAGTCTTAGACAGGATGCATGCGGTATTCTCTTGTATAATTAGAAGTTGAAAATA
CTTATATGCCTAGGAAGAGCTAGTGAGGGCGCAACCCTAGGCGTATCGCCTTGTCCTATTTTAAATTATACACCTCAATGTTATATAAAGGTTTAGAGTGAGTTAACAAGAGTATA

>TRINITY_DN37466_c0_g1_i1 from sample A6 / Example unspliced isoform:

AAAGAAAAGAGGGAGAACCGTTAGGGTTTCTCAAGAAGAGAAAAGTAGTTATGTTGAAGTAAAAGGGAGGCCGAAGGCTCTCTCTCAAGAAAAAGGTGTGCGACTATACCTTTGCACCAAAAAAAGGAGATGGAGGCTAGTTTGATAAGGACAAATGAGAGGAACTCAACGCAAATCAAAGAAGGAAGGGCACATTTCTA
TACCGGGTTTTGGAGATGgtaaatcgagcctggcaccagaccttaatactctggttgtttgtataattgtttatagagagcgtggtctctgcgatctcagtcatttcatttcttttgattactgcaagaaagtttgatctgctcactgtttaaaatgggagcaatcgctttcttttgcaactgtcattacttttgctagt
agagaaaagactcctcaacctctctccttttccttcaattgtttagtgcagaaagaaaggtcttgtatttgatgtctgaaataggaaaacctcatgtaaatacttgctactttctctttccatgactcgaataattaattctgttttatagCTATTCAATTTTGCAGATTGAATGTAAAGGAACTTTATAATTGTTCCTG
TATTCTGCCAGTGAAGAAAAGGGCGCAGCTCCTTTCGGAGCAAGCAACTCTTTCGGTAGTGTTCAAATTATTACTCATCCA

Intron 2 GTTGTTTGTA ... AATTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	20	4	2	0
A2	42.86	4	4	2
A3	100	0	2	2
A4	55.56	2	3	2
A5	33.33	5	4	1
A6	68.42	12	28	24
A7	43.82	25	31	8
A8	46.27	18	26	5
A9	43.82	25	23	16
A10	42.86	14	15	6

>TRINITY_DN38644_c0_g1_i4 from sample A9 / Example spliced isoform

GATTTTTAAAGAAAAGAGGGAGAACCGTTAGGGTTTCTCAAGAAGAGAAAAGTAGTTATGTTGAACTAAAAGGGAGGCCGAAGGCTCTCTCTCAAGAAAAAGGTGTGCGACTATACCTTTGCACCAAAAAAAGGAGATGGAGGCTAGTTTGATAAGGACAAATGAGAGGAACTCAACGCAAATCAAAGAAGGAAGGGCAC
ATTTCTATACCGGGTTTTGGAGATGGTAAATCGAGCCTGGCACCAGACCTTAATACTCTGATTGAATGTAAAGGAACTTTATAATTGTTCCTGTATTCTGCCAGTGAAGAAAAGGGCGCAGCTCCTTTCGGAGCAAGCAACTCTTTCGGAGATATCCTGCTACAGAACATGGAATGTGCGGCCTCCTGGCAGGAGAGCCA
GAGCCAGACCTCACTATTGGCTATCTTTTTATATATTATATACATGTACTTATATGCCTCTAGATGAAAGCCGCCCATTCTCCTAGATTGATATCTTTCAGTGCCTCTCCTTTGAGTTTTTAGATATGGTTTTATAAATGTGTGGACTGCCGCTCATGTGGGGGCAAGTCGCCTTTTCTTTTGTTAAACTGCTTGTGGTT
TTGACAAGAGCGTAGGGAGCGTCAATAACGGAGACTGCTCTTTATTTTTATATTTCTCTGTTGTTGATTATTGGCATTCTTCTTCTTGGATGAAGAAGAGAAGGGTAAAACCCTCCGCTAAAATTTATGTTTATATTTCTATATTAGATCTACAATAAATCAGCCTGAGCAAAGTCTTAGACAGGATGCATGCGGTATTC
TCTTGTATAATTAGAAGTTGAAAATACTTATATGCCTAGGAAGAGCTAGTGAGGGCGCAACCCTAGGCGTATCGCCTTGTCCTATTTTAA

>TRINITY_DN38644_c0_g1_i1 from sample A9 / Example unspliced isoform:

GATTTTTAAAGAAAAGAGGGAGAACCGTTAGGGTTTCTCAAGAAGAGAAAAGTAGTTATGTTGAACTAAAAGGGAGGCCGAAGGCTCTCTCTCAAGAAAAAGGTGTGCGACTATACCTTTGCACCAAAAAAAGGAGATGGAGGCTAGTTTGATAAGGACAAATGAGAGGAACTCAACGCAAATCAAAGAAGGAAGGGCAC
ATTTCTATACCGGGTTTTGGAGATGGTAAATCGAGCCTGGCACCAGACCTTAATACTCTGgttgtttgtataattgtttatagagagcgtggtctctgcgatctcagtcatttcatttcttttgattactgcaagaaagtttgatctgctcactgtttaaaatgggagcaatcgctttcttttgcaactgtcattacttt
tgctagtagagaaaagactcctcaacctctctccttttccttcaattgtttagtgcagaaagaaaggtcttgtatttgatgtctgaaataggaaaacctcatgtaaatacttgctactttctctttccatgactcgaataattaattctgttttatagctattcaattttgcagATTGAATGTAAAGGAACTTTATAATT
GTTCCTGTATTCTGCCAGTGAAGAAAAGGGCGCAGCTCCTTTCGGAGCAAGCAACTCTTTCGGTAGTGTTCAAATTATTACTCATCCTTTTAATTGTTTACCTTTAGTAAAATGGTTGAGGGCTTTGTCTTTTACGTAAACACTATTCAGCTTATTTAATGTAGTTGCAATAAGTTTTAGATTTTAATAACTTAAAA

Intron 3 GTAAATCGAG ... AATTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	29.86	14.7	11.5	1
A2	53.19	3.7	6	2.2
A3	50	3	4	2
A4	34.73	4	3	1.3
A5	49.88	4.2	3	3.5
A6	54.44	25.3	35.8	24.7
A7	43.97	33.5	41.5	11
A8	48.53	19.2	29	7
A9	61.85	14.2	25	19
A10	38.02	21.3	15	11

>TRINITY_DN37466_c0_g1_i2 from sample A6 / Example spliced isoform

AAAGAAAAGAGGGAGAACCGTTAGGGTTTCTCAAGAAGAGAAAAGTAGTTATGTTGAAGTAAAAGGGAGGCCGAAGGCTCTCTCTCAAGAAAAAGGTGTGCGACTATACCTTTGCACCAAAAAAAGGAGATGGAGGCTAGTTTGATAAGGACAAATGAGAGGAACTCAACGCAAATCAAAGAAGGAAGGGCACATTTCTA
TACCGGGTTTTGGAGATGATTGAATGTAAAGGAACTTTATAATTGTTCCTGTATTCTGCCAGTGAAGAAAAGGGCGCAGCTCCTTTCGGAGCAAGCAACTCTTTCGGAGATATCCTGCTACAGAACATGGAATGTGCGGCCTCCTGGCAGGAGAGCCAGAGCCAGACCTCACTATTGGCTATCTTTTTATATATTATATA
CATGTACTTATATGCCTCTAGATGAAAGCCGCCCATTCTCCTAGATTGATATCTTTCAGTGCCTCTCCTTTGAGTTTTTAGATATGGTTTTATAAATGTGTGGACTGCCGCTCATGTGGGGGCAAGTCGCCTTTTCTTTTGTTAAACTGCTTGTGGTTTTGACAAGAGCGTAGGGAGCGTCAATAACGGAGACTGCTCTT
TATTTTTATATTTCTCTGTTGTTGATTATTGGCATTCTTCTTCTTGGATGAAGAAGAGAAGGGTAAAACCCTCCGCTAAAATTTATGTTTATATTTCTATATTAGATCTACAATAAATCAGCCTGAGCAAAGTCTTAGACAGGATGCATGCGGTATTCTCTTGTATAATTAGAAGTTGAAAATACTTATATGCCTAGGAA
GAGCTAGTGAGGGCGCAACCCTAGGCGTATCGCCTTGTCCTATTTTAAATTATACACCTCAATGTTATATAAAGGTTTAGAGTGAGTTAACAAGAGTATA

>TRINITY_DN37466_c0_g1_i1 from sample A6 / Example unspliced isoform:

AAAGAAAAGAGGGAGAACCGTTAGGGTTTCTCAAGAAGAGAAAAGTAGTTATGTTGAAGTAAAAGGGAGGCCGAAGGCTCTCTCTCAAGAAAAAGGTGTGCGACTATACCTTTGCACCAAAAAAAGGAGATGGAGGCTAGTTTGATAAGGACAAATGAGAGGAACTCAACGCAAATCAAAGAAGGAAGGGCACATTTCTA
TACCGGGTTTTGGAGATGgtaaatcgagcctggcaccagaccttaatactctggttgtttgtataattgtttatagagagcgtggtctctgcgatctcagtcatttcatttcttttgattactgcaagaaagtttgatctgctcactgtttaaaatgggagcaatcgctttcttttgcaactgtcattacttttgctagt
agagaaaagactcctcaacctctctccttttccttcaattgtttagtgcagaaagaaaggtcttgtatttgatgtctgaaataggaaaacctcatgtaaatacttgctactttctctttccatgactcgaataattaattctgttttatagctattcaattttgcagATTGAATGTAAAGGAACTTTATAATTGTTCCTG
TATTCTGCCAGTGAAGAAAAGGGCGCAGCTCCTTTCGGAGCAAGCAACTCTTTCGGTAGTGTTCAAATTATTACTCATCCA

Intron 4 GTAGTGTTCA ... TTGCTTGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	45.45	3	2	3
A2	60	2	5	1
A3	33.33	1	0	1
A4	42.86	6	5	4
A5	27.27	12	0	9
A6	29.17	17	6	8
A7	13.33	13	1	3
A8	20	20	5	5
A9	27.27	16	8	4
A10	16	21	4	4

>TRINITY_DN111006_c0_g1_i2 from sample A1 / Example spliced isoform

AGAAAAAGGTGTGCGACTATACCTTTGCACCAAAAAAAGGAGATGGAGGCTAGTTTGATAAGGACAAATGAGAGGAACTCAACGCAAATCAAAGAAGGAAGGGCACATTTCTATACCGGGTTTTGGAGATGATTGAATGTAAAGGAACTTTATAATTGTTCCTGTATTCTGCCAGTGAAGAAAAGGGCGCAGCTCCTTTC
GGAGCAAGCAACTCTTTCGGAGATATCCTGCTACAGAACATGGAATGTGCGGCCTCCTGGCAGGAGAGCCAAAGCCAGACCTCACTATTGGCTATCTTTTTATATATTATATACATGTACTTATATGCCTCTAGATGAAAGCCGCCCATTCTCCTAGATTGATATCTTTCAGTGCCTCTCCTTTGAGTTTTTAGATATGG
TTTTATAAATGTGTGGACTGCCGCTCATGTGGGGGCAAGTCGCCTTTTCTTTTGTTAAACTGCTTGTGGTTTTGACAAGAGCGTAGGGAGCGTCAATAACGGAGACTGCTCTTTATTTTTATATTTCTCTGTTGTTGATTATTGGCATTCTTCTTCTTGGA

>TRINITY_DN111006_c0_g1_i1 from sample A1 / Example unspliced isoform:

AGAAAAAGGTGTGCGACTATACCTTTGCACCAAAAAAAGGAGATGGAGGCTAGTTTGATAAGGACAAATGAGAGGAACTCAACGCAAATCAAAGAAGGAAGGGCACATTTCTATACCGGGTTTTGGAGATGATTGAATGTAAAGGAACTTTATAATTGTTCCTGTATTCTGCCAGTGAAGAAAAGGGCGCAGCTCCTTTC
GGAGCAAGCAACTCTTTCGgtagtgttcaaattattactcatccttttaattgtttacctttagtaaaatggttgagggctttgtcttttacgtaaacactattcagcttatttaatgtagttgcaataagttttagattttaataacttaaaatccaacgatcaacaggcccactgcaaccccattaaatgagttgcag
caagctgaatagtcgctataatacccatatttctaatctttgattattttgttgcttgaagGAGATATCCTGCTACAGAACATGGAATGTGCGGCCTCCTGGCAGGAGAGCCAAAGCCAGACCTCACTATTGGCTATCTTTTTATATATTATATACATGTACTTATATGCCTCTAGATGAAAGCCGCCCATTCTCCTAGA
TTGATATCTTTCAGTGCCTCTCCTTTGAGTTTTTAGATATGGTTTTATAAATGTGTGGACTGCCGCTCATGTGGGGGCAAGTCGCCTTTTCTTTTGTTAAACTGCTTGTGGTTTTGACAAGAGCGTAGGGAGCGTCAATAACGGAGACTGCTCTTTATTTTTATATTTCTCTGTTGTTGATTATTGGCATTCTTCTTCTT
GGA