| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000730 | 1,064,254 | Δ1 bp | 100% | coding (235/1218 nt) | USA300HOU_1000 ← | LytR family transcriptional regulator |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,064,253 | 0 | C | . | 92.4% | 213.3 / 8.0 | 52 | coding (236/1218 nt) | USA300HOU_1000 | LytR family transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base C (2/1); new base . (18/30); total (20/32) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.53e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-01 | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
TAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGC > CP000730/1064116‑1064389 | tAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTcttt > 2:259567/1‑138 (MQ=255) aTCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCTtttt > 1:227900/1‑141 (MQ=255) tCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCtttttt > 2:225528/1‑141 (MQ=255) aaTAGCCAACTCTAGGAATTTAGTTTATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGCTCAGCATCCTGT‑CTTTTTTTCTTCTTcc < 2:218578/141‑1 (MQ=255) ccAACTTTAGGAATGTATGTGATATTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAACTCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGt < 2:514387/141‑1 (MQ=255) aaCTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTa < 2:389464/141‑1 (MQ=255) aCTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTat < 1:249559/141‑1 (MQ=255) tttAGGAATTTAGCTGATATTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTatca < 2:161185/141‑1 (MQ=255) tttAGGAATGCAGCTGAAAGTATCACGTGGAATACTAAGCATGCTAATTTGAGGTTTTGATTGATTAAAAGTAGTGAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTatca < 2:15958/141‑1 (MQ=255) aGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCg > 1:435037/1‑141 (MQ=255) aaTGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTACTTTGATGTTTTGCTTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGGGTTCAGCATCCGGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGAtc > 2:418315/1‑140 (MQ=255) gatcTGATAGGATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTa < 1:45400/138‑1 (MQ=255) gCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaag < 1:53584/141‑1 (MQ=255) gCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaag < 2:218191/141‑1 (MQ=255) tGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTTTTCTTCCATCGTTATCATCGATTCATaagaa > 1:218704/1‑141 (MQ=255) tGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaagaa > 2:139767/1‑141 (MQ=255) tGATAATAACACGTGGAATACTAAGCATTCTAAGTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGGGTGTTCAGCATCCGGT‑CTTTTTTTCTTCGTCCATCGTTATCATCGATACCTaagaa < 2:521455/141‑1 (MQ=255) gTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGTTACCTaagaaaagca > 2:303065/1‑139 (MQ=255) cGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCTTCGTTATCATCGATACCTAAGAAACGAATagagt > 1:521833/1‑140 (MQ=255) gAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTGTTCCATGGTTATCATCGATACCTAACAAAAGAATagagttcgg > 2:546180/1‑136 (MQ=255) aTACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgtt > 1:329742/1‑141 (MQ=255) aCTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCGTCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgttgt < 2:65139/141‑1 (MQ=255) tAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgttgttt > 2:173364/1‑140 (MQ=255) aaGCATTCTAATTTGATGTTTTGATTGATAAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATGTGTACCTAAGATAAGCATAGAGATAGGTCGttct > 2:237695/1‑141 (MQ=255) aGCATTCCAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGttctt < 1:197640/141‑1 (MQ=255) cATTCTTATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTTTTCg < 2:67493/141‑1 (MQ=255) cATTCTAATTTGATGTTTTTATTGATTAAAAGTAGTTNCAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCCTCGTTCTCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCg < 2:564468/141‑1 (MQ=255) aTTCTAATTTGATGTCTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGGTCTTCgg < 1:356451/141‑1 (MQ=255) ttCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCggg > 1:20544/1‑141 (MQ=255) ttAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGAt < 2:513534/140‑1 (MQ=255) tAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGAtt > 2:409484/1‑141 (MQ=255) aaTTTGATTTTTTGATGGATTAATAGTAGTTAGTATCATTGCGTCTTATCTAGTGTGTTCAGCATCCTTTCTTTTGTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGAtt < 1:400220/141‑1 (MQ=255) aTTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGa < 1:259567/141‑1 (MQ=255) aTTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGa > 1:569236/1‑141 (MQ=255) gATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATCCCTAAGAAAAGAATAGAGCTAGGTTGTTCATCGGGATTGACttt < 1:313362/141‑1 (MQ=255) aTGTTTTGATTGATTAAAAGTAGTTAAAGTCATGGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCAGCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTtta < 1:89387/141‑1 (MQ=255) attTAAAGTAGTTTAATTCATAGCTTCTCATCTAGAGTGTTCAGCATCCTCT‑CTCTTTCTCTTCTCCCATCGTTATCATCGATACCTAAGAAAAGAATAGACATAGGTTGTCCTTCGGGATTGACTTTATTATCTCTTAAg < 2:385678/141‑1 (MQ=255) ttAAAAGTATTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGt < 1:63343/141‑1 (MQ=255) ttAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGt < 1:480156/141‑1 (MQ=255) gtagtTAAAATCATAGCGTCTGCTCTAGAGTGTTCAGCTTCCTGT‑CTTTGTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATGGACTTTATTATCTCTTGAGTTGGAtt < 2:293662/141‑1 (MQ=255) gtTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTGCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGAc > 1:391625/1‑141 (MQ=255) gtTAAAATCATAGCGTCTGATCTAGAGTGTTCAGAATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAGAAGAATAGAGATAGGTTGTTCTTCGGGCTTGACTTTATTCTCTCTTGAGTTGGaggaac > 1:189373/1‑136 (MQ=255) acaaaTCATTGCGTCTGATCTTGAGTGTTCAGCATCCT‑TTCTTTTTTTCGTCTTTCATCGTTATCATCGATACCTAAGAAAAGAATACAGATAGGTTGTTCGTCTGGATTCACTTTCTTATCACTTTAGTTGGATTGACGa < 2:347766/139‑1 (MQ=255) aaaTCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGAtt < 1:106624/141‑1 (MQ=255) gCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCAtttt < 1:187631/141‑1 (MQ=255) gTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTATTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGAAGATTAGCATTTTTg < 1:317039/141‑1 (MQ=255) tGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTg > 1:62039/1‑141 (MQ=255) aTCTAGAGTGTTCCGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTc < 1:475339/141‑1 (MQ=255) gagTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTgag < 2:227900/141‑1 (MQ=255) gtgtTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGagaa < 1:313660/141‑1 (MQ=255) cAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTc > 2:350725/1‑141 (MQ=255) aTCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTCTTGTCTTGAGAAGATTCGAAt > 2:561135/1‑141 (MQ=255) ccTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGc < 1:409484/141‑1 (MQ=255) | TAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGAATGC > CP000730/1064116‑1064389 |
| 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: ‑ |