NA ----> NA

Intron 1 GTATGTATGG ... CTTTGTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	71.43	6	13	17
A2	60	2	0	6
A3	100	0	4	6
A4	88.24	1	9	6
A5	78.95	2	4	11
A6	-1	0	0	0
A7	100	0	0	2
A8	0	1	0	0
A9	100	0	0	1
A10	11.11	4	0	1

>TRINITY_DN108800_c1_g1_i9 from sample A5 / Example spliced isoform

AAAAAATTAGCACAGAGGATAGCAATTTGTTTGATGAGTCCAAGGAATTTGTCTATGGCCAAGCACACATAGCGAGTGACTACACTTTGAGACCTAAGAAGGCCGAGTGGAGAAGATACCATAAATATTGAAAATTCAATGCAGAGTATTGTATAGAGGATTGTTGGGTCCTGTTATTATTTTAGCAAAGTGAATGAAAT
TTTCTTTGTTGCACTATTATTTCTTTTATGAATACATTGATTATATTGTTGCTAAGACATGTACATTTAGTTCAAAAAGTTAATATTATTTGAAATATAAATAGAATGGTTCTTGCCTTCAACTCTCTAGTTTGACCTATATGATGACTCCAATATATTATTATGGATTTGTTGCAGATGGCTTATTTTGGGAGTCATGC
GTATACAAAATGGACTTTCTATCTTTATGAAACAAACTCTAAGGGATGTATGTTTCCTACTATGAAAAATGATTGGCTTTGAAAGATTTTTACCATTTCTAATACTCGATACTTTTTTTCTTTCAGGGGAAGAAAGCACATTGTAGGAAAGATGATGTACGG

>TRINITY_DN108800_c1_g1_i10 from sample A5 / Example unspliced isoform:

AAAAAATTAGCACAGAGGATAGCAATTTGTTTGATGAGTCCAAGGAATTTGTCTATGGCCAAGCACACATAGgtatgtatggcaattcatcattctatttatttgctatttaaattcctcgaatattttgtttattcatttggtatcatgcttgaactatatgctttgtgcagCGAGTGACTACACTTTGAGACCTAAGA
AGGCCGAGTGGAGAAGATACCATAAATATTGAAAATTCAATGCAGAGTATTGTATAGAGGATTGTTGGGTCCTGTTATTATTTTAGCAAAGTGAATGGAATTTTCTTTGTTGCACA

Intron 2 GTATGTATGG ... CTTTGTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	66.67	14	30	26
A2	35.06	25	12	15
A3	47.69	17	17	14
A4	64	9	15	17
A5	53.85	9	10	11
A6	11.11	4	1	0
A7	20	2	1	0
A8	-1	0	0	0
A9	-1	0	0	0
A10	100	0	2	4

>TRINITY_DN114454_c1_g1_i9 from sample A3 / Example spliced isoform

GGTTTCTTGAGTTTAAGCATGGCCATGCTTTGTTTAGTTTGTCATGTGTTATGAATATTTCTCTTTGTTTTGCAATTTTTTTATGGTTTGGTTTTGCTTGTTTTGGCTGGGAGGAGTGGTACAAATAGTATACAAAAGAGATGAAATGGAGATTATTGTTCAAATATGAAGTCATTGCAGTTGTAGAATCTAAGGTGGAG
TGGTGAAAATGCCTTGCAAATGGAAAAAGTAGTGCGGAGGATAGAGACATTATATTGTTGTTGTTATCACGTTGATTTATCTGATGAGTCCACAGACATTGGCAATGACCAAGCAAACATGGCGAGTGACTGTACACTTTGGGCCCTAAGAAAGCCGAGTGGAGAATATACCATAAATATTTAAAATTTATGGCAGAGGA
TTG

>TRINITY_DN114454_c1_g1_i24 from sample A3 / Example unspliced isoform:

TGTAGAATGATTTACCCTTTGTCATGGTTACGGGGCACTATCATGTTGCTAATGGTTGGGTGATTCAAAAGTTTCTTGGAATTATTGGAGTGGAGAAGATACCATAAATATTGTAGAGACATTATATTGTTGTTGTTATCACGTTGATTTATCTGATGAGTCCACAGACATTGGCAATGACCAAGCAAACATGGgtatgt
atggtaattcatcattctatctctgtgttatttaatttcttggaattttttgtttattcattggctcatactcaaactatattctttgtgtagCGAGTGACTGTACACTTTGGGCCCTAAGAAGGCCGAGTGGAGAATATACCATAAATATTTAAAATTTATGGCAGAGGATTGGTGGGTCCTGTTATTGTTTTGCAAAA
TAACATTATTTTGTAAGCGAATGAAATATTCTTTGTTGCACGGTTATTTCTATTATGAATATTTTGATTATATTGTTCCTTGTAGACGTAC

Intron 3 GTAATTCATC ... CTTTGTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	66.1	10	18	21
A2	41.03	23	18	14
A3	56.7	21	29	26
A4	67.74	10	21	21
A5	79.49	4	18	13
A6	100	0	3	0
A7	0	1	0	0
A8	100	0	2	2
A9	50	1	1	1
A10	-1	0	0	0

>TRINITY_DN123229_c2_g1_i7 from sample A1 / Example spliced isoform

GAGTGACAACAATTTGGGCCTTAAGAAGGGCTAGTGGAGAAGATGCTATAAACATTGCAAACTCATGGCATGAGATCGCAGATGGCCTATTTTGGGAATCATGAGTGTACAAAATGAACTTTCTATCTTTATAAAACAAACTCGAAGGGAAGAAAGCACATTGCAGAAAAGATGATGTACGAAGAGAGGAAGTTTGCAAT
TTTTTGTTTATTGTTTTTTGTGTCCTTTCGTTTTCATGAGTTTAAGCATGGCCATGCTTTCTTTCATTTGTCGTGTTATGATTTGTTTTCTTTGTTTTGCATTTTTTTGTGGTATGGTTTTGGTTTAGTTTGCTTGTTGGCGAGAGGGGGAAAGTGGTAAAAATAGTATATAGAAGAGATGAGATGGGGATTATTGTTCA
AACATGAAGAATCTAAGAAGGTGGAGTGGTGAAGATGCCTTGTAAATGGAAAAAGTAGCACATAAGATAGGTAAATCATGCTTTTCTCCTAGAAACTAATGTTGTCATTTAACTGAATGAAATATTGTTGTTTATAGAACGATTTACCCTTTTTTCATGGTTACGGAACACTATCATGTTGCTAATGGGTGAGCGATTCA
AAATTTTCTTGGAATTCTCAGACATTATAATGTGGTTGAAATGTTTATATTGTTCAAGGCTTATTGTTTCTGGTTGTCTCTGTTATCATGTTAATTTGTGTTTGATGATTCCAAGGAAGTTGGCAACAACCCAGCACACAGAGTTATGTATGTGAGTGACAACAATTTGGGCCCTAAGAAGGTCGAGTGGAGAAGATACC
ATAACCATTGTAACTCATTGCACATGATTGGTGATTCCTGTTATTGTTTTGCAAATTAGAATTATTTCGGAAGGGAATGAAATATTATTTGTTGCAATGTTATTTATCTTATGAATACGTTGATTAAATTGTTGCTAATA

>TRINITY_DN123229_c2_g1_i2 from sample A1 / Example unspliced isoform:

GAGTGACAACAATTTGGGCCTTAAGAAGGGCTAGTGGAGAAGATGCTATAAACATTGCAAACTCATGGCATGAGATCGCAGATGGCCTATTTTGGGAATCATGAGTGTACAAAATGAACTTTCTATCTTTATAAAACAAACTCGAAGGGAAGAAAGCACATTGCAGAAAAGATGATGTACGAAGAGAGGAAGTTTGCAAT
TTTTTGTTTATTGTTTTTTGTGTCCTTTCGTTTTCATGAGTTTAAGCATGGCCATGCTTTCTTTCATTTGTCGTGTTATGATTTGTTTTCTTTGTTTTGCATTTTTTTGTGGTATGGTTTTGGTTTAGTTTGCTTGTTGGCGAGAGGGGGAAAGTGGTAAAAATAGTATATAGAAGAGATGAGATGGGGATTATTGTTCA
AACATGAAGAATCTAAGAAGGTGGAGTGGTGAAGATGCCTTGTAAATGGAAAAAGTAGCACATAAGATAGGTAAATCATGCTTTTCTCCTAGAAACTAATGTTGTCATTTAACTGAATGAAATATTGTTGTTTATAGAACGATTTACCCTTTTTTCATGGTTACGGAACACTATCATGTTGCTAATGGGTGAGCGATTCA
AAATTTTCTTGGAATTCTCAGACATTATAATGTGGTTGAAATGTTTATATTGTTCAAGGCTTATTGTTTCTGGTTGTCTCTGTTATCATGTTAATTTGTGTTTGATGATTCCAAGGAAGTTGGCAACAACCCAGCACACAGAGTTATGTATGgtaattcatctttatatctatttgttatttaatttcctggaatttatg
gtttaattgtggtttcatactcgaactatatgctttgtgcagTGAGTGACAACAATTTGGGCCCTAAGAAGGTCGAGTGGAGAAGATACCATAACCATTGTAACTCATTGCACATGATTGGTGATTCCTGTTATTGTTTTGCAAATTAGAATTATTTCGGAAGGGAATGAAATATTATTTGTTGCAATGTTATTTATCTT
ATGAATACGTTGATTAAATTGTTGCTAATA

Intron 4 GTGGGTCAAT ... CTTTGTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	71.88	9	33	13
A2	95.56	1	35	8
A3	63.08	12	28	13
A4	70.37	8	24	14
A5	71.43	6	20	10
A6	36.84	6	5	2
A7	100	0	2	0
A8	33.33	2	0	2
A9	0	5	0	0
A10	-1	0	0	0

>TRINITY_DN108800_c1_g1_i19 from sample A5 / Example spliced isoform

CAGTTGTAGAGTCTAAGAAGGTTTAGTGGTGACGATGCCTTGCAAATAGAAAGATGTAGCACAAAGGGTAGTGAGTGACAACAATTTGGGCCTCAAGAAGGGCTAGTGGAGAAGATGCTATAAACATTGCAAACTCATGGCATGAGATCGATGGCCTATTTTGGGAATCATGAGTGTACAAAATGAACTTTCTATCTTTA
TAAAACAAACTCGAAGGGAAGAAAGCACATTGCAGAAACGATGATGTAGGAAGAGAGGAAGTTTG

>TRINITY_DN108800_c1_g1_i12 from sample A5 / Example unspliced isoform:

CAGTTGTAGAGTCTAAGAAGGTTTAGTGGTGACGATGCCTTGCAAATAGAAAGATGTAGCACAAAGGGTAGgtgggtcaatcttttctcctacaaactaatcttgtcatttaactgaatgaaatattgttgtttgtagaatgatttacccttttgtcatggttattgggcactatcatgtttctaatgggtgagtgattc
aaaagttttctggaatttgcataggcattttttgggggttgaaatgtttatattgttcaggacttattgtttctggttgtctctgttatcatgttgatttttgtctgatgattccaaggaagttggcaatggtaattcatcattctgtctatctgttattaatttccttgaatttatggtttaattgtggttgcatactc
aaactatatgctttgtgtagTGAGTGACAACAATTTGGGCCTCAAGAAGGGCTAGTGGAGAAGATGCTATAAACATTGCAAACTCATGGCATGAGATCGATGGCCTATTTTGGGAATCATGAGTGTACAAAATGAACTTTCTATCTTTATAAAACAAACTCGAAGGGAAGAAAGCACATTGCAGAAACGATGATGTAGGA
AGAGAGGAAGTTTG