NA ----> NA

Intron 1 GTTTAGCGAG ... TCGCTGGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	45.24	23	18	20
A2	74.39	8.8	32.8	18
A3	48.32	30.8	36.5	21
A4	54.17	23	31.8	22.6
A5	28.59	7.6	3	3
A6	51.29	32.6	40.4	28.3
A7	48.96	54.6	63.8	41
A8	56.03	25.1	32	32
A9	43.14	54.1	42	40
A10	49.48	47.3	67.6	25

>TRINITY_DN116176_c0_g1_i2 from sample A1 / Example spliced isoform

GAGAAACAGGTGAAAACGGAGTTAAATGGAATGCTGGGAGGTACTGATCGGAGCAAATCAATGGCGTTGCGGCTGACAAAACACGCTCTTCATCGCAGTTTGAGCATAACCAGCAGGGCCGTCCATGGAAGCACGGCTCTGAGGTCCATAGTAGAACATTCCTGAACAATACAGCACTATCGCTGGCACTCCTCTCTGCC
AAAGAGAATTATTTTCAAGTCTCTGTAATGCTGAAGATTTTCCTCTACTATTTTCTCTTTTCGACTCAAAGCGAGTGAAGTCAACTTTCAAAGAACTCAACCTGTGTACATGACAAAAGTTTTGCAAGTTTGATATATCTAAGAAGCACTCTAAAAAGTGGTATTAATCTTTGCTAAATTTCAGAGAAACCATGGATGAT
GATGGACCAATGGAGGAAACTATCTTGGTTGGTGATGACCTTATGTTGGGACCCCCATCACCTCTTATTCCCCCAGATATCGCATCTCATGTACTTGAAGGTGTTGAGCTTTGTGATGGTATTTTGAAGAAACTTTTCCTTTGTTTGCAGGTAAATGATATTGAACCCTTTTGTCAAGATGAGATTGCTTTATATCGACG
TTGTGCAGAAGAACGGGATAAGGAAATCAGGCGTCGCATCCAAGAAAGTGAAAGAAAATTAGGGCAATTGATGCCCGAGGAGCGTGCAAAGGAGCGAACTGTTCAACTTCAATCAGAAGTTACATCGTTGGAAAGGCGCTTAATTCTCGCTAGTGGAATGCAAGGCATGGAAGGATTCCGTCAACGTTGGAGTTTACATG
GTCGCCTTCAAGACACAAAAAAAAGACTAGAAGCTTTGGAGAAAGGTTTGGAAAAGAGAAAGGAGGAAAAGGGGAATATTCAAGAGCTGCAGGGAAAAAAGGGATGGCGCTTTTGGAAGTGACTAATGATGAACTAAAATATCTAGCATTCTTAACAATAGGCAAAGTTTGTTACTTACAATTGAATTGCAACCTAGTAG
AAATTACTGCTCATTCATTCTGTTGATATTCAAGTCTGTTTATATTACTAAGCAGTGTCTTTCTTGTATATTTAATTCGTGATAAGAGTTAGAAAATGCATGAATTGCCCAAGGAAATCAAGTGAGGCTATTATTTTTATCACCAGTAGCCAGTTAGAATTGTCTGGTATTTTTCTTTTTCATAACCTGAAAAACAATAT
GAAAGAAAACAAAGCATCTCTTTTCCATTCTTGTTGGCAAACAAATTACATGAATTGGAAAAGATATTAAATAAGATAACAGTTGGGTAGGCG

>TRINITY_DN116176_c0_g1_i4 from sample A1 / Example unspliced isoform:

GAGAAACAGGTGAAAACGGAGTTAAATGGAATGCTGGGAGGTACTGATCGGAGCAAATCAATGGCGTTGCGGCTGACAAAACACGCTCTTCATCGCAGgtttagcgagtaaattacaggttatgtgtgactgtgtttcaatggtttgcagcggcctttcagattcagaatcgactgtgttgtcgccgattctaacttctt
tctgtccgttgtatttctcgctggaagTTTGAGCATAACCAGCAGGGCCGTCCATGGAAGCACGGCTCTGAGGTCCATAGTAGAACATTCCTGAACAATACAGCACTATCGCTGGCACTCTCTGCCAAAGAGAATTATTTTCAAGTCTCTGTAATGCTGAAGATTTTCCTCTACTATTTTCTCTTTTCGACTCAAAGCGA
GTGAAGTCAACTTTCAAAGAACTCAACCTGTGTACATGACAAAAGTTTTGCAAGTTTGATATATCTAAGAAGCACTCTAAAAAGTGGTATTAATCTTTGCTAAATTTCAGAGAAACCATGGATGATGATGGACCAATGGAGGAAACTATCTTGGTTGGTGATGACCTTATGTTGGGACCCCCATCACCTCTTATTCCCCC
AGATATCGCATCTCATGTACTTGAAGGTGTTGAGCTTTGTGATGGTATTTTGAAGAAACTTTTCCTTTGTTTGCAGGTAAATGATATTGAACCCTTTTGTCAAGATGAGATTGCTTTATATCGACGTTGTGCAGAAGAACGGGATAAGGAAATCAGGCGTCGCATCCAAGAAAGTGAAAGAAAATTAGGGCAATTGATGC
CCGAGGAGCGTGCAAAGGAGCGAACTGTTCAACTTCAATCAGAAGTTACATCGTTGGAAAGGCGCTTAATTCTCGCTAGTGGAATGCAAGGCATGGAAGGATTCCGTCAACGTTGGAGTTTACATGGTCGCCTTCAAGACACAAAAAAAAGACTAGAAGCTTTGGAGAAAGGTTTGGAAAAGAGAAAGGAGGAAAAGGGG
AATATTCAAGAGCTGCAGGGAAAAAAGGGATGGCGCTTTTGGAAGTGACTAATGATGAACTAAAATATCTAGCATTCTTAACAATAGGCAAAGTTTGTTACTTACAATTGAATTGCAACCTAGTAGAAATTACTGCTCATTCATTCTGTTGATATTCAAGTCTGTTTATATTACTAAGCAGTGTCTTTCTTGTATATTTA
ATTCGTGATAAGAGTTAGAAAATGCATGAATTGCCCAAGGAAATCAAGTGAGGCTATTATTTTTATCACCAGTAGCCAGTTAGAATTGTCTGGTATTTTTCTTTTTCATAACCTGAAAAACAATATGAAAGAAAACAAAGCATCTCTTTTCCATTCTTGTTGGCAAACAAATTACATGAATTGGAAAAGATATTAAATAA
GATAACAGTTGGGTAGGCG

Intron 2 GTTATGTGTG ... TCGCTGGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	47.61	18.7	14	20
A2	64.27	14.4	33.7	18
A3	52.39	22.3	28	21
A4	52.13	25.1	32	22.6
A5	29.25	4.9	1	3
A6	44.24	44.1	41.6	28.3
A7	46.98	59.9	64.9	41
A8	52.65	29.7	34	32
A9	41.19	59.4	43	40
A10	51.6	41	61.7	25

>TRINITY_DN116176_c0_g1_i6 from sample A1 / Example spliced isoform

GAGAAACAGGTGAAAACGGAGTTAAATGGAATGCTGGGAGGTACTGATCGGAGCAAATCAATGGCGTTGCGGCTGACAAAACACGCTCTTCATCGCAGGTTTAGCGAGTAAATTACAGTTTGAGCATAACCAGCAGGGCCGTCCATGGAAGCACGGCTCTGAGGTCCATAGTAGAACATTCCTGAACAATACAGCACTAT
CGCTGGCACTCCTCTCTGCCAAAGAGAATTATTTTCAAGTCTCTGTAATGCTGAAGATTTTCCTCTACTATTTTCTCTTTTCGACTCAAAGCGAGTGAAGTCAACTTTCAAAGAACTCAACCTGTGTACATGACAAAAGTTTTGCAAGTTTGATATATCTAAGAAGCACTCTAAAAAGTGGTATTAATCTTTGCTAAATT
TCAGAGAAACCATGGATGATGATGGACCAATGGAGGAAACTATCTTGGTTGGTGATGACCTTATGTTGGGACCCCCATCACCTCTTATTCCCCCAGATATCGCATCTCATGTACTTGAAGGTGTTGAGCTTTGTGATGGTATTTTGAAGAAACTTTTCCTTTGTTTGCAGGTAAATGATATTGAACCCTTTTGTCAAGAT
GAGATTGCTTTATATCGACGTTGTGCAGAAGAACGGGATAAGGAAATCAGGCGTCGCATCCAAGAAAGTGAAAGAAAATTAGGGCAATTGATGCCCGAGGAGCGTGCAAAGGAGCGAACTGTTCAACTTCAATCAGAAGTTACATCGTTGGAAAGGCGCTTAATTCTCGCTAGTGGAATGCAAGGCATGGAAGGATTCCG
TCAACGTTGGAGTTTACATGGTCGCCTTCAAGACACAAAAAAAAGACTAGAAGCTTTGGAGAAAGGTTTGGAAAAGAGAAAGGAGGAAAAGGGGAATATTCAAGAGCTGCAGGGAAAAAAGGGATGGCGCTTTTGGAAGTGACTAATGATGAACTAAAATATCTAGCATTCTTAACAATAGGCAAAGTTTGTTACTTACA
ATTGAATTGCAACCTAGTAGAAATTACTGCTCATTCATTCTGTTGATATTCAAGTCTGTTTATATTACTAAGCAGTGTCTTTCTTGTATATTTAATTCGTGATAAGAGTTAGAAAATGCATGAATTGCCCAAGGAAATCAAGTGAGGCTATTATTTTTATCACCAGTAGCCAGTTAGAATTGTCTGGTATTTTTCTTTTT
CATAACCTGAAAAACAATATGAAAGAAAACAAAGCATCTCTTTTCCATTCTTGTTGGCAAACAAATTACATGAATTGGAAAAGATATTAAATAAGATAACAGTTGGGTAGGCG

>TRINITY_DN116176_c0_g1_i4 from sample A1 / Example unspliced isoform:

GAGAAACAGGTGAAAACGGAGTTAAATGGAATGCTGGGAGGTACTGATCGGAGCAAATCAATGGCGTTGCGGCTGACAAAACACGCTCTTCATCGCAGGTTTAGCGAGTAAATTACAGgttatgtgtgactgtgtttcaatggtttgcagcggcctttcagattcagaatcgactgtgttgtcgccgattctaacttctt
tctgtccgttgtatttctcgctggaagTTTGAGCATAACCAGCAGGGCCGTCCATGGAAGCACGGCTCTGAGGTCCATAGTAGAACATTCCTGAACAATACAGCACTATCGCTGGCACTCTCTGCCAAAGAGAATTATTTTCAAGTCTCTGTAATGCTGAAGATTTTCCTCTACTATTTTCTCTTTTCGACTCAAAGCGA
GTGAAGTCAACTTTCAAAGAACTCAACCTGTGTACATGACAAAAGTTTTGCAAGTTTGATATATCTAAGAAGCACTCTAAAAAGTGGTATTAATCTTTGCTAAATTTCAGAGAAACCATGGATGATGATGGACCAATGGAGGAAACTATCTTGGTTGGTGATGACCTTATGTTGGGACCCCCATCACCTCTTATTCCCCC
AGATATCGCATCTCATGTACTTGAAGGTGTTGAGCTTTGTGATGGTATTTTGAAGAAACTTTTCCTTTGTTTGCAGGTAAATGATATTGAACCCTTTTGTCAAGATGAGATTGCTTTATATCGACGTTGTGCAGAAGAACGGGATAAGGAAATCAGGCGTCGCATCCAAGAAAGTGAAAGAAAATTAGGGCAATTGATGC
CCGAGGAGCGTGCAAAGGAGCGAACTGTTCAACTTCAATCAGAAGTTACATCGTTGGAAAGGCGCTTAATTCTCGCTAGTGGAATGCAAGGCATGGAAGGATTCCGTCAACGTTGGAGTTTACATGGTCGCCTTCAAGACACAAAAAAAAGACTAGAAGCTTTGGAGAAAGGTTTGGAAAAGAGAAAGGAGGAAAAGGGG
AATATTCAAGAGCTGCAGGGAAAAAAGGGATGGCGCTTTTGGAAGTGACTAATGATGAACTAAAATATCTAGCATTCTTAACAATAGGCAAAGTTTGTTACTTACAATTGAATTGCAACCTAGTAGAAATTACTGCTCATTCATTCTGTTGATATTCAAGTCTGTTTATATTACTAAGCAGTGTCTTTCTTGTATATTTA
ATTCGTGATAAGAGTTAGAAAATGCATGAATTGCCCAAGGAAATCAAGTGAGGCTATTATTTTTATCACCAGTAGCCAGTTAGAATTGTCTGGTATTTTTCTTTTTCATAACCTGAAAAACAATATGAAAGAAAACAAAGCATCTCTTTTCCATTCTTGTTGGCAAACAAATTACATGAATTGGAAAAGATATTAAATAA
GATAACAGTTGGGTAGGCG

Intron 3 GTATGAATCT ... TCTGGAGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	10.71	25	3	0
A2	30	21	9	2
A3	34.38	21	11	0
A4	40.91	13	9	0
A5	9.09	10	1	0
A6	20	36	9	0
A7	20.74	53.5	14	0
A8	9.62	47	5	0
A9	18.19	40.5	9	0
A10	12.55	55.8	8	0

>TRINITY_DN106917_c0_g1_i4 from sample A3 / Example spliced isoform

GGCAAACAAATTACCTCCCCTCATATGTTTAGGGGCAGAGAAACAGGTGAAAACGGAGTTAAATGGAATGCTGGGAGGTACTGATCGGAGCAAATCAATGGCGTTGCGGCTGACAAAACACGCTCTTCATCGCAGTTTGAGCATAACCAGCAGGGCCGTCCATGGAAGCACGGCTCTGAGGTCCATAGTAGAACATTCCT
GAACAATACAGCACTATCGCTGGCACTCCTCTCTGCCAAAGAGAATTATTTTCAAGTCTCTGTAATGCTGAAGATTTTCCTCTACTATTTTCTCTTTTCGACTCAAAGCGAGTGAAGTCAACTTTCAAAGAACTCAACCTGTGTACATGACAAAAGTTTTGCAAGTTTGATATATCTAAGAAGCACTCTAAAAAGTGGTA
TTAATCTTTGCTAAATTTCAGAGAAACCATGGATGATGATGGACCAATGGAGGAAACTATCTTGGTTGGTGATGACCTTATGTTGGGACCCCCATCACCTCTTATTCCCCCAGATATCGCATCTCATGTACTTGAAGGTGTTGAGCTTTGTGATGGTATTTTGAAGAAACTTTTCCTTTGTTTGCAGGTAAATGATATTG
AACCCTTTTGTCAAGATGAGATTGCTTTATATCGACGTTGTGCAGAAGAACGGGATAAGGAAATCAGGCGTCGCATCCAAGAAAGTGAAAGAAAATTAGGGCAATTGATGCCCGAGGAGCGTGCAAAGGAGCGAACTGTTCAACTTCAATCAGAAGTTACATCGTTGGAAAGGCGCTTAATTCTCGCTAGTGGAATGCAA
GGCATGGAAGGATTCCGTCAACGTTGGAGTTTACATGGTCGCCTTCAAGACACAAAAAAAAGACTAGAAGCTTTGGAGAAAGGTTTGGAAAAGAGAAAGGAGGAAAAGGGGAATATTCAAGAGCTGCAGGGAAAAAAGGGATGGCGCTTTTGGAAGTGACTAATGATGAACTAAAATATCTAGCATTCTTAACAATAGGC
AAAGTTTGTTACTTACAATTGAATTGCAACCTAGTAGAAATTACTGCTCATTCATTCTGTTGATATTCAAGTCTGTTTATATTACTAAGCAGTGTCTTTCTTGTATATTTAATTCGTGATAAGAGTTAGAAAATGCATGAATTGCCCAAGGAAATCAAGTGAGGCTATTATTTTTATCACCAGTAGCCAGTTAGAATTGT
CTGGTATTTTTCTTTTTCATAACCTGAAAAACAATATGAAAGAAAACAAAGCATCTCTTTTCCATTCTTGTTGGCAAACAAATTACATGAATTGGAAAAGATATTAAATAAGATAACAGTTGGGCGG

>TRINITY_DN106917_c0_g1_i7 from sample A3 / Example unspliced isoform:

GGCAAACAAATTACCTCCCCTCATATGTTTAGGGGCAGAGAAACAGGTGAAAACGGAGTTAAATGGAATGCTGGGAGGTACTGATCGGAGCAAATCAATGGCGTTGCGGCTGACAAAACACGCTCTTCATCGCAGGTTTAGCGAGTAAATTACAGGTTATGTGTGACTGTGTTTCAATGGTTTGCAGCGGCCTTTCAGAT
TCAGAATCGACTGTGTTGTCGCCGATTCTAACTTCTTTCTGTCCGTTGTATTTCTCGCTGGAAGTTTGAGCATAACCAGCAGGGCCGTCCATGGAAGCACGGCTCTGAGGTCCATAGTAGAACATTCCTGAACAATACAGCACTATCGCTGGCACTCCTCTCTGCCAAAGAGAATTATTTTCAAGTCTCTGTAATGCTGA
AGATTTTCCTCTACTATTTTCTCTTTTCGACTCAAAGCGAGTGAAGTCAACTTTCAAAGAACTCAACCTGTGTACATGACAAAAGTTTTGCAAGTTTGATATATCTAAGAAGCACTCTAAAAAGTGGTATTAATCTTTGCTAAATTTCAGAGAAACCATGGATGgtatgaatcttttcactctctagaccttataaattt
atgtgccttttcaataatatcttgatctagattctgaacagatgatagctcatccataaggttcaaatgtgtaaaatttaattagttgattacttcagagcacataatttatttttaatatgcatcttccaattccattttcacaaatgttaaggatattgtttaccatcttgattctggagtagATGATGGACCAATGG
AGGAAAC