sp|Q9LPZ1|MORF9_ARATH ----> Multiple organellar RNA editing factor 9, chloroplastic

Intron 1 GTATGTATGC ... TTGGTTTTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	0	23.1	1	0
A2	65.26	3.6	0	3
A3	45.48	11	0	3
A4	0	14.4	0	0
A5	0	13.9	0	0
A6	25.13	40.1	0	3
A7	29.58	57	0	6
A8	6.91	30.6	0	1
A9	0	70.4	0	0
A10	12.34	62.3	0	2

>TRINITY_DN47154_c0_g1_i15 from sample A7 / Example spliced isoform

AAACATTTGGCTCCCTCGTTACTAAAATCACAGCGGCAAAAACCCTACCTGTGGTTGCTCTCACTCTCGTACAAGGCAGTCATGTCACCCCGTCTGTTTCTCCTCCGGACCCTTGCCCGGGCAAGGGCTTTCTCCACAACTTCATCAACGTTCTCTGCTCATTCTTCTTCACCTGCTCTGCTACCTAAATCATCTTCCTT
CCCTGTTCTCTCAGGTTACGGCCATTTATGCGGGTTTAATCGGCCATCACCGCCGTCGCGATGTATGATTGTTCGTTGCCGGGTTTCGAACTCCGGATCTGTGTACTCTCCGCTAGACTCCAATGATTCCGGCAGGCGAGAACCTCTTTTCCCAGGCTGCGACTATGAACATTGGCTCGTCACCATGGAGTTTCCAGACC
CCCAAACTACCCGTGAACAAAAGATCGACACTTTTGTCAAGACGCTTGCTAACGTTGTCGGAAGCGAAGAGAAGGCGAAAAAAAGAATATATGTGCTATCGACAACAACTTACACTGGATTTATGTGTGAAATTTCCGAGGAACTTTCAGAAAAAATCAAGAAGGAGCCTGGCGTTGAATGGGTGCTGCCGGATTCCTAC
GGAGACCCCATAAAGAAGGAGTATGGCGTTGGAGATAAGTACATAAATGGAGTGATCATACCTGATACAAGGGTCTATAATAGGCCAACTGGTAGGGACAGGCCCCGAAATCGAAGAAGAGATTCAATGCCTATCGAGCGGAGAGATGTACAAACATCCAGGGATCCTCTGCCACCATTAGGTGGAAGAGACACCATACA
GGGCAATAGTGTGCAGGGTGACCAACGGGATTTTAGGCCAACAGAAAGTAGGGACAGCATGCAAGGGGGTCAAAGGGTCTACAGACCTATGGATGGAAGAGCCCCAATGTCAGGTGATGGACAAGACTACAGGCCGCTTGTGGATTCAAGAGGTCCATTGCTGGGAAATCGACCAGACTATAGGCCACCTGTGGATGCAA
GGGGTCCAGTGCCAGGATTTCAACAAGATTACAGACCACCTGTGGATGGAAGGGGTCCAATGCCGGGATATCGACAAGACTTCAGGCCACCTGCGGATGCAAGGGGCCCATTGCCTGGAAACCAGCAAGACTACAGGCCACCTGTGGATGCAAGAGGTCCGATGCCAGGATACAGGCAAGACTACAGGCCACCTTTGGAT
GAAAGAGGCTCGATGTCAGGAGTGCGACCAGATTACAGGCCACCTGTGGATCCAAGAGGCCCAATGCCGGGAGGCCAGCCAAACTACAGTCCACCTGTGGAAGGAGGAAGGGGTTGGATGCCAGGTGACCGTCAAGATTACATGCCACCAGTGGAAGGAGGAGGCTCAGTATCGGGAGGGAGCAGAGATTACATACCTTC
TAGAGAATCAACGCAGGGTCAACAAAGAGACTCAATGGGAGTACAAGGCGAAGATCCAGTGCGTTTTGTATTATCCAAGGTTGAATGCACTCTCAAACTCAAGACAAGTGTTGGTGTGAAGGTTTGTGGAGACAAGTTCTTTAAGACTCACACCAGCCCTGGTACCTCTTCACCTCATGGCACCTCAAGGCTTTCAATCG
TTTGCAAGAGATGGGACATTACATGGAATGTGGGATTAATTCAAGTGTGAGTATGTATGTCACCCTGATGAATAGCTGGGATATTTGCTCGAGAAGTATGGATATATCTAACACCGTTGGGATGCTCCTCTGCCCATTCTATGTTTCCTGTCCAGGGCTTGTCTTTGATGCTGGATTAACCATTTCATGCAGAGGATAAT
ACAAAATAATCAATACTGCATTTACTTCATAATTTCAGAAAACATTATCCACCCAAATCATTGTGCACTGTGTGCAGTCTCTAACCTGCATAGAAGAATTAGGCGTTGGAAGGAAAAAATGCAAGAATGCCATGGTTTACTAGTCAGGAAATTAGATAAATGGACGAAATTTTTGCGAGAGAGGACAGGGGGTGAAAAAT
ACTCTTGGAACCAGCAATTGGAGGATGTGGAATCCCAACTGGAAAGCTTGAAATTGAGGCAACAAAGACTGAAATTACAAGAGGCAATAACAACATTCGTCTTGAAGAAATGGAAGAGAAGTTGAAAGGAGTACTGGAGAAAGTGGAGCAATTTGAAGCAAGAAGGAAATTGGCAAGGGAAGTGGCACATTCATATTCTC
CTCCACCACATTCTGATGGATTCTATGGGCCAGAGCAGTGGAGACTCGGAGAGAAGCCAAGGAGGCAACAATACAGCAAGCATTGCTTCGTGAATTGAACAAGTCTGAGCAGGCCCAGGTCTCCAAGGTTGGTGGAAAGAGCCATTGTGGGAAAGCTCCTTTTTAAATTCTAGTGTTAGTACATGGTTTGCAAGTATGTT
TTGTTAGTAAAGCAGTTTGTCAGGCATTTGACATGTCGTCTGGAATGTAATAGATGTAGTACATCGAGCTAGTTAAGGAAGTTAGCAGAGCAAAACTTTTTATGGACTCTTTTTGGAACATTAAAGACTAGGTCTTCCAATTTCTGTTCGGTCGCAGCTTCATTTTAATACAAATATATCAGTTTCTATTATTGTTTTTT
AAACAATTTGAAAAGATAATGGCCATTTAGAACGATGCTAAATTTTGGATTTTTATCCACT

>TRINITY_DN47154_c0_g1_i12 from sample A7 / Example unspliced isoform:

GGAACTTTCAGAAAAAATCAAGAgtatgtatgcagacctggttgattaagttttagcttattttacctacattattatggtgcgaatagatacaattttagtttccaaatttatgtttagatttatgtagatttcggttttagagttttaataatttccaaattttcgggttcagagtttcaatcttttgtttagatttt
ggtagctttcggtttcagactcttagttagctaccattagtaaaaacaattataccattagtaaaaacaattatctgattggttttagAGGAGCCTGGCGTTGAGTTCTCTGTTCTTTCCACAATTTCAGCATGTCACGGTTGAAGAGAAAGAGGGCATGTGAGGGCGGGCATGCATTTTGTGTGAAGTACGCCTAAATA
ATGGATCAAGTAAAGTGATTGTCCGTTCCACCGAAAATGGCATGTTTTTGGTATTTGCAATTGCAATTTGTCTTAATTTCTTTTGTCCCCTAGTAAAATAGCACATGTGTTGGGTAGAATATTAAATTTTCCCAGTGCTGATGATGTGGTAAGCATAATGTGCTAATGTCTGTCATAGTTGAGAATAAAATTGCTAAATA
ATTCAGATATATGTCAGTGCTAGAATCTGGAAAAAGCTTATAAATTTGTTTGTTCATTAACATCACCTTATTTCTGATTTTGTTTGTCACAATTTTCTGGCTGTATAAGAACTTCTCTCAGACATGGA

Intron 2 GTTGTCGGAC ... CAATTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	35.99	18	9	11.2
A2	16.43	25.5	4	6
A3	16.67	32.7	7	6
A4	21.21	28	13	2
A5	26.75	19.7	10	4
A6	18.89	59	20	7.3
A7	20.44	91.2	38	8.5
A8	22.81	66.2	28	11
A9	21.58	85.3	36	10.7
A10	24.11	78	42	6.5

>TRINITY_DN43412_c0_g2_i2 from sample A6 / Example spliced isoform

CTTCCGAAAAATGTTCTGAAATATTGTCTCGAAGTTCGAAGTTCAAACCAGAAGCATGGCATTAAGGTTACAGCCATTTATGCGGGTTTAATCGGCCACCACCGCCGTCGCGATGCATGATTGTTCGTTGTTGGGTTTCGAACTCTGGATCTGTGTACTCTCCCCTAGACTCCAATGATTCCGGCAGACGAGAACCTCTT
TTCCCAGGCTGCGACTATGAACATTGGCTCGTCACCATGGAGTTTCCAGACCCCCAAACTACCCGTGAACAAAAGATCGACACTTCTGTCAAGACGGTTGCTAACCGAAGAGAAGGCGAAAAAAAGAATATATGTGCTATCGACAACAACTTACACTGGATTTATGTGTGAAATTTCCGAGGAACTTTCAGAAAAAATCA
AGAGTATGTATGCAGACCTGGTTGATTAAGTTTTAGCTTATTTTACCTACATTATTATGGTGCGAATAGATACAATTTTAGTTTCCAAATTTATGTTTAGATTTGTGTAGATATCGGTTTTCGAGTTTTAATAAT

>TRINITY_DN43412_c0_g2_i4 from sample A6 / Example unspliced isoform:

CTTCCGAAAAATGTTCTGAAATATTGTCTCGAAGTTCGAAGTTCAAACCAGAAGCATGGCATTAAGGTTACAGCCATTTATGCGGGTTTAATCGGCCACCACCGCCGTCGCGATGCATGATTGTTCGTTGTTGGGTTTCGAACTCTGGATCTGTGTACTCTCCCCTAGACTCCAATGATTCCGGCAGACGAGAACCTCTT
TTCCCAGGCTGCGACTATGAACATTGGCTCGTCACCATGGAGTTTCCAGACCCCCAAACTACCCGTGAACAAAAGATCGACACTTCTGTCAAGACGGTTGCTAACgttgtcggacggttttaactcttcactggtggttttcttcttgtgtttgaaatatacattcgaggggttttggggaaattgaattgtttgaatat
aaagattcgaagtcttgttagccatcttcttctcgtccttaaaacatacacttctagggtttgtggggaaatttggaaggcagaaatagcttacaaaaacatttttaatcgattgacacatgcaagttgcatgaataacccatattttcttttgtcaattcgcagttgcttgaataacccatgttttctttcgccaattt
gcaatcttcagttgcttgaacacccatattttcttttgccaatttgcagCGAAGAGAAGGCGAAAAAAAGAATATATGTGCTATCGACAACAACTTACACTGGATTTATGTGTGAAATTTCCGAGGAACTTTCAGAAAAAATCAAGAGTTGGAGACTACTATGAGGAACTCACCTGCTTGGCCATAGGTGATAGCATATG
GGAGCTTATAACAATAAAAATTACTATATAGACCTGCTTCTGCCATAACTATTGTTGAGACAGATTGTGAGGTGGATTCTGCTCCTCCTGGTGATTACAAAGAACCAGAAAGAGCACCATCCAAGCCTGCTCCTTTTCCAAGCACAACAGTATCTTAAGGTCTGTATGGGTTGGCCTTTTTTTCCCTTTCATTTGCTGCC
TTCCATTAGAAACCTTTGTTCAAAATTGAAGTGGAGGACAAATAGGAATTCTACACAAATTGAGCACTTTGATCTAAG

Intron 3 GTAAAGTGAT ... TTTGTCACAG

Found issues: Low number of reads

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	53.57	3	4	3
A2	100	0	8	2
A3	50	1	2	0
A4	55	1	1	1.5
A5	50	1	0	2
A6	100	0	6	3
A7	77.13	2	9	4.5
A8	56.47	4	7	3.5
A9	-1	0	0	1
A10	100	0	7	0

>TRINITY_DN43860_c0_g1_i14 from sample A8 / Example spliced isoform

AGGAGCCTGGCGTTGAGTTCTCTGTTCTTTCCACAATTTCAGCATGTCACGGTTGAAGAGAAAGAGGGCATGTGAGGGCGGGCATGCATTTTGTGTGAAGTACGCCTAAATAATGGATCAATTTTCTGGCTGTATAAGAACTTCTCTCAGACATGGAGACAGATGAAAGATGTAAAACAAGATGTAAGAAAGTCAAAACT
CATCACTTTAAATAAAAATAATTGTAATTTTTATGAAGGGGTAATTGGGGCTGAGAAACTTAAAGTATTGATTAGGAAGATGGAATATTTTTTTAAGATGGGAATTTTTTTTTTAAATGAAATTGCAG

>TRINITY_DN43860_c0_g1_i10 from sample A8 / Example unspliced isoform:

GTTTTAATAATTTCCAAATTTTCGGGTTCAGAGTTTCAATCTTTTGTTTAGATTTTGGTAGCTGTCGGTTTCAGACTCTTAGTTAGCTACCATTAGTAAAAACAATTATACCATTAGTAAAAACAATTATCTGATTGGTTTTAGAGGAGCCTGGCGTTGAGTTCTCTGTTCTTTCCACAATTTCAGCATGTCACGGTTGA
AGAGAAAGAGGGCATGTGAGGGCGGGCATGCATTTTGTGTGAAGTACGCCTAAATAATGGATCAAgtaaagtgattgtacattccaccgaaaatggcatgtttttggtattaacaattgcaatttatcttaatttcttttgttccctagtaaaatagcacatgtgttgggtagaatattaaattttcccagtgctgatga
tgtggtaagcataatgtgctaatgtctgtcatagttgagaataaaattgctaaataattcagatatatgtcagtgctagaatctggaaaaagcttataaatttgtttgttcattaacatcaccttatttctaattttgtttgtcacagTTTTCTGGCTGTATAAGAACTTCTCTCAGACATGGAGACAGATGAAAGATGT
AAAACAAGATCATCTCTACGCATAGATTATCCAATGCTTTTTAAGCTTCATAATCCAGTAACGCAACGTACATCACACTGTGGAGTATGTGAGTTTCTTGTTGAGGAGGGAATGATTTAAATGCCATATTGGGTTGGAGACTACTATGAGGAACTCACTTGCTTGGCCATAGGTGATAGCATATGGGAGCTTATAACAAT
AAAAATTTACTAGATAGACATAGTTGAGGCAAAACCTGCTTCTGCCATAACTATTGTTGAGACAGATTGTGAGGTGGATTCTGCTCCTCCTGGTGATTACAAAGAACCAGAAAGAGCACCATCCAAGCCTGCTCCTTTTCCAAGCACAACAGTATCTCAAG

Intron 4 GTAAGTTGCT ... TTGATTATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	65.22	56	103	107
A2	71.19	35	87	86
A3	71.72	42	101	112
A4	70.91	24	64	53
A5	68.81	17	37	38
A6	70.03	356	863	801
A7	70.27	316	806	688
A8	69.04	474	1116	998
A9	70.34	314	804	685
A10	71.47	202	522	490

>TRINITY_DN104557_c0_g1_i8 from sample A4 / Example spliced isoform

CTCGTTACTAAAATCACAGCGGCGAAAACCCTACCTGTGGTTGCTCTCACTCTCGTACAAGGCAGTCATGTCACCCCGTCTGTTTCTCCTCCGGACCCTTGCCCGGGCAAGGGCTTTCTCCACAACTTCATCAACGTTCTCTGCTCATTCTTCTTCACCTGCTCTGCTACCTAAATCATCTTCCTTCCCTGTTCTCTCAG
GTTACGGCCATTTATGCGGGTTTAATCGGCCATCACCGCCGTCGCGATGTATGATTGTTCGTTGCCGGGTTTCGAACTCCGGATCTGTGTACTCTCCGCTAGACTCCAATGATTCCGGCAGGCGAGAACCTCTTTTCCCAGGCTGCGACTATGAACATTGGCTCGTCACCATGGAGTTTCCAGACCCCCAAACTACCCGT
GAACAAAAGATCGACACTTTTGTCAAGACGCTTGCTAACGTTGTCGGAAGCGAAGAGGAGGCGAAAAAAAGAATATATGCGCTATCGACAACAACTTACACTGGATTTATGTGTGAAATTTCCGAGGAACTTTCAGAAAAAATCAAGAAGGAGCCTGGCGTTGAATGGGTGCTGCCGGATTCCTACGGAGACCCCATAAA
GAAGGAGTATGGCGTTGGAGATAAGTACATAAATGGAGTGATCATACCTGATACAAGGGTCTATAATAGGCCAACTGGTAGGGACAGGCCCCGAAATCGAAGAAGAGATTCAATGCCTATCGAGCGGAGAGATGTACAAACATCCAGGGATCCTCTGCCACCATTAGGTGGAAGAGACACCATACAGGGCAATAGTGTGC
AGGGTGACCAACGGGATTTTAGGCCAACAGAAAGTAGGGACAGCATGCAAGGGGGTCAAAGGGTCTACAGACCTATGGATGGAAGAGCCCCAATGTCAGGTGATGGACAAGACTACAGGCCGCCTGTGGATTCAAGAGGTCCATTGCCGGGAAATCGACCAGACTATAGGCCACCTGTGGATGCAAGGGGTCCAGTGCCA
GGATTTCAACAAGATTACAGACCACCTGTGGATGGAAGGGGTCCAATGCCGGGATATCGACAAGACTTCAGGCCACCTGCGGATGCAAGGGGCCCATTGCCTGGAAACCAGCAAGACTACAGGCCACCTGTGGATGCAAGAGGTCCGATGCCAGGATACAGGCAAGACTACAGGCCACCTTTGGATGAAAGAGGCTCGAT
GTCAGGAGTGCGACCAGATTACAGGCCACCTGTGGATCCAAGAGGCCCAATGCCGGGAGCCCAGCCAAACTACAGGCCACCTATGGAAGGAGGAAGGGGTTGGATGCCAGGTGACCGTCAAGATTACATGCCACCAGTGGAAGGAGGAGGCTCAGTATCGGGAGGGAGCAGAGATTACATACCTTCTAGAGAACCAATGC
AGGGTCAACAAAGAGACTCAATGGGAGTACAAGGCGAAGATCCAGTGCGTGTGGTGTAAGGGGAGCGTTTTCCATGACCAATGGAGCAAATTAATTCAGCATGTCTGTATGCAAGAGAAGAATTTCGAGTGGAATGTAAGTTAATGAGGACTATCATACATGCATGGGTGAACAGAAGGGGAGTGCAGCTGTTGGGGGTT
GTTCTCCTTGTAATGTTTAATTCCGGTCTGCCCTTTTTTGTTCATTGAATAGGATTAGTGGTTTGCAAGGTGTAGGTGAGTGGCCTTTTAGCTTAGTTGTTACTAGACTATAAGATTTATATTAATATTCATTCTGTTCAGGGACATGTGTGATGCAAGGAATGAACACTTGATATAATTATTTTGGAAGTCACCAATTT
GTATTTTATATAGATGTGTGTCAATTATTGGTAAGTTTGATTGTGTCTATTTATTAAAAAAATTAAAAAAC

>TRINITY_DN104557_c0_g1_i2 from sample A4 / Example unspliced isoform:

CTCGTTACTAAAATCACAGCGGCGAAAACCCTACCTGTGGTTGCTCTCACTCTCGTACAAGGCAGTCATGTCACCCCGTCTGTTTCTCCTCCGGACCCTTGCCCGGGCAAGGGCTTTCTCCACAACTTCATCAACGTTCTCTGCTCATTCTTCTTCACCTGCTCTGCTACCTAAATCATCTTCCTTCCCTGTTCTCTCAG
GTTACGGCCATTTATGCGGGTTTAATCGGCCATCACCGCCGTCGCGATGTATGATTGTTCGTTGCCGGGTTTCGAACTCCGGATCTGTGTACTCTCCGCTAGACTCCAATGATTCCGGCAGGCGAGAACCTCTTTTCCCAGGCTGCGACTATGAACATTGGCTCGTCACCATGGAGTTTCCAGACCCCCAAACTACCCGT
GAACAAAAGATCGACACTTTTGTCAAGACGCTTGCTAACGTTGTCGGAAGCGAAGAGGAGGCGAAAAAAAGAATATATGCGCTATCGACAACAACTTACACTGGATTTATGTGTGAAATTTCCGAGGAACTTTCAGAAAAAATCAAGAAGGAGCCTGGCGTTGAATGGGTGCTGCCGGATTCCTACGGAGACCCCATAAA
GAAGGAGTATGGCGTTGGAGATAAGTACATAAATGGAGTGATCATACCTGATACAAGGGTCTATAATAGGCCAACTGGTAGGGACAGGCCCCGAAATCGAAGAAGAGATTCAATGCCTATCGAGCGGAGAGATGTACAAACATCCAGGGATCCTCTGCCACCATTAGGTGGAAGAGACACCATACAGGGCAATAGTGTGC
AGGGTGACCAACGGGATTTTAGGCCAACAGAAAGTAGGGACAGCATGCAAGGGGGTCAAAGGGTCTACAGACCTATGGATGGAAGAGCCCCAATGTCAGGTGATGGACAAGACTACAGGCCGCCTGTGGATTCAAGAGGTCCATTGCCGGGAAATCGACCAGACTATAGGCCACCTGTGGATGCAAGGGGTCCAGTGCCA
GGATTTCAACAAGATTACAGACCACCTGTGGATGGAAGGGGTCCAATGCCGGGATATCGACAAGACTTCAGGCCACCTGCGGATGCAAGGGGCCCATTGCCTGGAAACCAGCAAGACTACAGGCCACCTGTGGATGCAAGAGGTCCGATGCCAGGATACAGGCAAGACTACAGGCCACCTTTGGATGAAAGAGGCTCGAT
GTCAGGAGTGCGACCAGATTACAGGCCACCTGTGGATCCAAGAGGCCCAATGCCGGGAGCCCAGCCAAACTACAGGCCACCTATGGAAGGAGGAAGGGGTTGGATGCCAGGTGACCGTCAAGATTACATGCCACCAGTGGAAGGAGGAGGCTCAGTATCGGGAGGGAGCAGAGATTACATACCTTCTAGAGAACCAATGC
AGGGTCAACAAAGAGACTCAATGGGAGTACAAGGCGAAGATCCAGTGCGTGTGGTGTAAGGGGAGCGTTTTCCATGACCAATGGAGCAAATTAATTCAGCATGTCTGTATGCAAGAGAAGAATTTCGAGTGGAATgtaagttgcttgcaaaatttgagctggaaatgtataaacattcgtctcatcccttctgtggaaat
atctgacttttttgattatagGTAAGTTAATGAGGACTATCATACATGCATGGGTGAACAGAAGGGGAGTGCAGCTGTTGGGGGTTGTTCTCCTTGTAATGTTTAATTCCGGTCTGCCCTTTTTTGTTCATTGAATAGGATTAGTGGTTTGCAAGGTGTAGGTGAGTGGCCTTTTAGCTTAGTTGTTACTAGACTATAAG
ATTTATATTAATATTCATTCTGTTCAGGGACATGTGTGATGCAAGGAATGAACACTTGATATAATTATTTTGGAAGTCACCAATTTGTATTTTATATAGATGTGTGTCAATTATTGGTAAGTTTGATTGTGTCTATTTATTAAAAAAATTAAAAAAC

Intron 5 GCAAGTTGCA ... CAATTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	51.18	17.2	24	11.2
A2	45.5	8.4	8	6
A3	70.61	3.8	11	6
A4	42.95	9	11	2
A5	55.09	7.8	15	4
A6	42.89	14.6	11	8.4
A7	43.51	30	37	8
A8	47.05	18.8	22	10.8
A9	45.84	21.6	24	10.6
A10	38.28	12.6	4	6.6

>TRINITY_DN119380_c0_g1_i14 from sample A2 / Example spliced isoform

TTGTGTTTGAAATATACATTCGAGGGGTTTTGGGGAAATTGAATTGTTTGAATATAAAGATTCGAAGTCTTGTTAGCCATCTTCTTCTCGTCCTTAAAACATACACTTCTAGGGTTTGTGTGGAAATTTGGAAGGCAGAAATAGCTTACAAAAACATTTTTAATCGATTGACACATCGAAGAGAAGGCGAACAAAAGAAT
ATATGCGCTATCGACAACAACTTACACTGGATTTATGTGTGAAATTTCCGAGGAACTTTCAGAAAAAATCAAGAAGGAGCCTGGCGTTGAATGGGTGCTGCCGGATTCCTACGGAGACCCCATAAAGAAGGAGTATGGCGTTGGAGATAAGTACATAAATGGAGTGATCATACCTGATACAAGGGTCTATAATAGGCCAA
CTGGTAGGGACAGGCCCCGAAATCGAAGAAGAGATTCAATGCCTATCGAGCGGAGAGATGTACAAACATCCAGGGATCCTCTGCCACCATTAGGTGGAAGAGACACCATACAGGGCAATAGTGTGCAGGGTGACCAATGGGATTTTAGGCCAACAGAAAGTAGGGACAGCATGCAAGGGGGTCAAAGGGTCTACAGACCT
ATGGATGGAAGAGCCCCAATGTCAGGTGATGGACAAGACTACAGGCCGCCTGTGGATTCAAGAGGTCCATTGCCGGGAAATCGACCAGACTATAGGCCACCTGTGGATGCAAGGGGTCCAGTGCCAGGATTTCAACAAGATTACAGACCACCTGTGGATGGAAGGGGTCCAATGCCGGGATATCGACAAGACTTCAGGCC
ACCTGCGGATGCAAGGGGCCCATTGCCTGGAAACCAGCAAGACTACAGGCCACCTGTGGATGCAAGAGGTCCGATGCCAGGATACAGGCAAGACTACAGGCCACCTTTGGATGAAAGAGGCTCGATGTCAGGAGTGCGACCAGATTACAGGCCACCTGTGGATCCAAGAGGCCCAATGCCGGGAGCCCAGCCAAACTACA
GGCCACCTATGGAAGGAGGAAGGGGTTGGATGCCAGGTGACCGTCAAGATTACATGCCACCAGTGGAAGGAGGAGGCTCAGTATCGGGAGGGAGCAGAGATTACATACCTTCTAGAGAACCAATGCAGGGTCAACAAAGAGACTCAATGGGAGTACAAGGCGAAGATCCAGTGCGTTTTGTATTATCCAAGGTTGAATGC
ACTCTCAAACTCAAGACAAGTGTTGGTGTGAAGGTTTGTGGAGACAAGTTCTTTAAGACTCACACCAGCCCTGGTACCTCTTCACCTCATGGCACCTCAAGGCTTTCAATCGTTTGCAAGAGATGGGACATTACATTGAATGTGGGATTAATTCAAGTGTGAGTATGTATGTCACCCTGATGAATAGCTGGGATATTTGC
TCGAGAAGTATGGATATATCTAACACCGTTGGGATGCTCCTCTGCCCATTCTATGTTTCCTGTCCAGGGCTTGTCTTTGATGCTGGATTAACCATTGCATGCAGAGGATAATCTCTGCTCTCAATTTGCATCAGTATCTCAGGTATGATGGAGAATTTGGGTTTTTCAGAGGATCTTGTAACCAATGTGGAGGATCTTTG
GTTTGGGAAGACATTATTGAAAACATATCCACCCAAATCATTGTGCACTGTGTGCAGTCTCTAACCTGCATAGAAGAATTAGGCGTTGGAAGGAAAAAATGCAAGAATGCCATGGTTTACTAGTCAGGAAATTAGATAAATGGACGAAATTTTTGCGAGAGAGGACAGGGGGTGAAAAATACTCTTGGAACCAGCAATTG
GAGGATGTGGAATCCCAACTGGAAAGCTTGAAATTGAGGCAACAAAGACTGAAATTACAAGAGGCAATAACAACATTCGTCTTGAAGAAATGGAAGAGAAGTTGAAAGGAGTACTGGAGAAAGTGGAGCAATTTGAAGCAAGAAGGAAATTGGCAAGGGAAGTGGCACATTCATATTCTCCTCCACCACATTCTGATGGA
TTCTATGGGCCAGAGCAGTGGAGACTCGGAGAGAAGCCAAGGAGGCAACAATACAGCAAGCATTGCTTCGTGAATTGAACAAGTCTGAGCAGGCCCAGGTCTCCAAGGTTGGTGGAAAGAGCCATTGTGGGAAAGCTCCTTTTTAAATTCTAGTGTTAGTACATGG

>TRINITY_DN119380_c0_g1_i9 from sample A2 / Example unspliced isoform:

TTGTGTTTGAAATATACATTCGAGGGGTTTTGGGGAAATTGAATTGTTTGAATATAAAGATTCGAAGTCTTGTTAGCCATCTTCTTCTCGTCCTTAAAACATACACTTCTAGGGTTTGTGTGGAAATTTGGAAGGCAGAAATAGCTTACAAAAACATTCTTAATCGATTGACACATgcaagttgcatgaataacccatat
tttcttttgtcaattcgcagttgcttgaataacccatgttttctttcgccaatttgcaatcttcagttgcttgaacacccatattttcttttgccaatttgcagCGAAGAGAAGGCGAAAAAAAGAATATATGTGCTATCGACAACAACTTACACTGGATTTATGTGTGAAATTTCCGAGGAACTTTCAGAAAAAAATCA
AGAAGGAGCCTGGCGTTGAGTTCTCTGTTCTTTCCACAATTTCAGCATGTCACGGTTGAAGAGAAAGAGGGCATG

Intron 6 GTTCTCTGTT ... ACAATTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	20	4	0	2
A2	100	0	3	5
A3	100	0	2	2
A4	-1	0	0	0
A5	0	1	0	0
A6	25	3	1	1
A7	42.86	6	5	4
A8	33.33	5	2	3
A9	0	13	0	0
A10	50	4	2	6

>TRINITY_DN47154_c0_g1_i5 from sample A7 / Example spliced isoform

TTTTTATCATGCCATTCTTCCGAAAAATGTTCTGAAATATTGTCTCGAAGTTCGAAGTTCAAACCAGAAGCATGGCATTAAGGTTACAGCCATTTATGCGGGTTTAATCGGCCACCACCGCCGTCGCGATGCATGATTGTTCGTTGTTGGGTTTCGAACTCTGGATCTGTGTACTCTCCCCTAGACTCCAATGATTCCGG
CAGACGAGAACCTCTTTTCCCAGGCTGCGACTATGAACATTGGCTCGTCACCATGGAGTTTCCAGACCCCCAAACTACCCGTGAACAAAAGATCGACACTTCTGTCAAGACGGTTGCTAACGTTGTCGGACGGTTTTAACTCTTCACTGCGAAGAGAAGGCGAAAAAAAGAATATATGTGCTATCGACAACAACTTACAC
TGGATTTATGTGTGAAATTTCCGAGGAACTTTCAGAAAAAATCAAGAAGGAGCCTGGCGTTGACATGTCACGGTTGAAGAGAAAGAGGGCATGCATTTTGTGTGAAGTACGCCTAAATAATGGATCAATTTTCTGGCTGTATAAGAACTTCTCTCAGACATGGAGACAGATGAAAGATGTAAAACAAGATGTAAGAAAGT
CAAAACTCATCACTTTAAATAAAAATAATTGTAATTTTTATGAAGGGGTAATTGGGGCTGAGAAACTTAAAGTATTGATTAGGAAGATGGAATATTTTTTTAAGATGGGAATTTTTTTTTTAAATGAAATTGCAGGA

>TRINITY_DN47154_c0_g1_i12 from sample A7 / Example unspliced isoform:

GGAACTTTCAGAAAAAATCAAGAGTATGTATGCAGACCTGGTTGATTAAGTTTTAGCTTATTTTACCTACATTATTATGGTGCGAATAGATACAATTTTAGTTTCCAAATTTATGTTTAGATTTATGTAGATTTCGGTTTTAGAGTTTTAATAATTTCCAAATTTTCGGGTTCAGAGTTTCAATCTTTTGTTTAGATTTT
GGTAGCTTTCGGTTTCAGACTCTTAGTTAGCTACCATTAGTAAAAACAATTATACCATTAGTAAAAACAATTATCTGATTGGTTTTAGAGGAGCCTGGCGTTGAgttctctgttctttccacaatttcagCATGTCACGGTTGAAGAGAAAGAGGGCATGTGAGGGCGGGCATGCATTTTGTGTGAAGTACGCCTAAATA
ATGGATCAAGTAAAGTGATTGTCCGTTCCACCGAAAATGGCATGTTTTTGGTATTTGCAATTGCAATTTGTCTTAATTTCTTTTGTCCCCTAGTAAAATAGCACATGTGTTGGGTAGAATATTAAATTTTCCCAGTGCTGATGATGTGGTAAGCATAATGTGCTAATGTCTGTCATAGTTGAGAATAAAATTGCTAAATA
ATTCAGATATATGTCAGTGCTAGAATCTGGAAAAAGCTTATAAATTTGTTTGTTCATTAACATCACCTTATTTCTGATTTTGTTTGTCACAATTTTCTGGCTGTATAAGAACTTCTCTCAGACATGGA

Intron 7 GTTTTAACTC ... CAATTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	26.53	27	8	11.5
A2	15.15	28	4	6
A3	12.82	34	4	6
A4	17.95	32	12	2
A5	22.58	24	10	4
A6	15.12	73	19	7
A7	14.55	113	30	8.5
A8	19.15	76	25	11
A9	16.38	111	33	10.5
A10	16.5	100	33	6.5

>TRINITY_DN42016_c1_g2_i11 from sample A9 / Example spliced isoform

CGAGAACCTCTTTTCCCAGGCTGCGACTATGAACATTGGCTCGTCACCATGGAGTTTCCAGACCCCCAAACTACCCGTGAACAAAAGATCGACACTTCTGTCAAGACGGTTGCTAACGTTGTCGGACGCGAAGAGAAGGCGAAAAAAAGAATATATGTGCTATCGACAACAACTTACACTGGATTTATGTGTGAAATTTC
CGAGGAACTTTCAGAAAAAATCAAGATTTTCTGGCTGTATAAGAACTTCTCTCAGACATGGAGACAGATGAAAGATGTAAAACAAGATCATCTCTACGCATAGATTATCCAA

>TRINITY_DN42016_c1_g2_i9 from sample A9 / Example unspliced isoform:

TGCCATTCTTCCGAAAAATGTTCTGAAATATTGTCTCGAAGTTCGAAGTTCAAACCAGAAGCATGGCATTAAGGTTACAGCCATTTATGCGGGTTTAATCGGCCACCACCGCCGTCGCGATGCATGATTGTTCGTTGTTGGGTTTCGAACTCTGGATCTGTGTACTCTCCCCTAGACTCCAATGATTCCGGCAGACGAGA
ACCTCTTTTCCCAGGCTGCGACTATGAACATTGGCTCGTCACCATGGAGTTTCCAGACCCCCAAACTACCCGTGAACAAAAGATCGACACTTCTGTCAAGACGGTTGCTAACGTTGTCGGACGgttttaactcttcactggtggttttcttcttgtgtttgaaatatacattcgaggggttttggggaaattgaattgtt
tgaatataaagattcgaagtcttgttagccatcttcttctcgtccttaaaacatacacttctagggtttgtggggaaatttggaaggcagaaatagcttacaaaaacatttttaatcgattgacacatgcaagttgcatgaataacccatattttcttttgtcaattcgcagttgcttgaataacccatgttttctttcg
ccaatttgcaatcttcagttgcttgaacacccatattttcttttgccaatttgcagCGAAGAGAAGGCGAAAAAAAGAATATATGTGCTATCGACAACAACTTACACTGGATTTATGTGTGAAATTTCCGAGGAACTTTCAGAAAAAATCAAGATTTTCTGGCTGTATAAGAACTTCTCTCAGACATGGAGACAGATGAA
AGATGTAAAACAAGATCATCTCTACGCATAGATTATCCAA