| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 355,466 | G→A | 100% | P412S (CCA→TCA) | brnQ_2 ← | Branched‑chain amino acid transport system 2 carrier protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 355,466 | 0 | G | A | 93.1% | 36.6 / ‑3.2 | 15 | P412S (CCA→TCA) | brnQ_2 | Branched‑chain amino acid transport system 2 carrier protein |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (5/8); total (7/8) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.29e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.84e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
ATATAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGGTACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCGATA > USA300TCH1516_ALE/355338‑355601 | atatAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATAcaagccaagc > 1:479283/1‑141 (MQ=255) tAGTAACGATGGGTCAAGCATTACTGGGAAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAGTACATCGATTATGAAACCGATAATAGCACCGCACCTGAACACTACAACGCAAGCTAAGTCGATAACt > 1:218630/1‑141 (MQ=255) cAACCATTACTAGGCAGTAAGCATTTATTAAGTGGTCGCTTGTTTCGGACGGCGTATAAATACACCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAAcat < 1:4052/141‑1 (MQ=255) aCTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACg < 1:140509/141‑1 (MQ=255) gTGAGCACTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCaaa > 1:361704/1‑141 (MQ=255) gTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGtaat < 1:210142/141‑1 (MQ=255) cGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGtt > 1:15768/1‑141 (MQ=255) ttCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTa < 1:455739/141‑1 (MQ=255) ggACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTGAAAGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTAttt > 1:132671/1‑141 (MQ=255) gACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGGTACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACAACGTGTAATAAGTTGAAACTATTTa > 1:35927/1‑141 (MQ=255) aCCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGt < 1:166568/141‑1 (MQ=255) aCCGATAATAGCAAAGAGCATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGt < 1:47823/141‑1 (MQ=255) aaGAGCATGAATGATACAAGCCAAGCTAAATCCATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCg < 1:195909/141‑1 (MQ=255) gacATGAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACCATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGt < 1:204776/139‑1 (MQ=255) gAATGATACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGCCGATa > 1:63376/1‑141 (MQ=255) | ATATAAAAAAGCCTAGTAACGATGGGTCAATCATTACTAGGCAGTGAGCATTTATTAAGTTGTCGCTTGTTTCGGACGGCGTATAAATACATCGATTATGAAACCGATAATAGCAAAGAGCATGAATGGTACAAGCCAAGCTAAATCGATATCTGCTAAAGGTAACATCATAAACGATTTCAAAATAACACCGTGTAATAAGTTGAAACTATTTAGTATTTGTAAAATTGAAATAATCAATGTAATAACAGTTGCGAGTCGATA > USA300TCH1516_ALE/355338‑355601 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |