| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 3,199,794 | 0 | C | T | 31.8% | 112.9 / 25.1 | 64 | intergenic (‑179/‑28) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base C (2/41); new base T (20/0); total (23/41) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.71e-14 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
AAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGA > CP009273/3199657‑3199925 | aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTc < 1:632516/138‑1 (MQ=255) aCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGa < 1:2908871/139‑1 (MQ=255) tGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTGAGTGGTAGTTTGTGGCGGTTAATTTTTTCCGACaaa > 1:1129778/1‑139 (MQ=255) aTTCCCTGCGCTGGCGCAATATTCATTCTTATTTGCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTCTCCATACAAATACa < 1:3301398/139‑1 (MQ=255) ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAAATTTTTCAGACAAAAACaa > 1:1258542/1‑139 (MQ=255) cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGacaaaaacaaaa > 1:1082056/1‑139 (MQ=255) ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGACCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCa < 1:1592456/121‑1 (MQ=255) tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTgg < 1:2998478/138‑1 (MQ=255) ctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑g < 1:3713141/139‑1 (MQ=255) atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAAAAAAAAACGGA‑GTTGC‑Catg > 1:1536972/1‑139 (MQ=255) ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCg < 1:4277299/139‑1 (MQ=255) tcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAg < 1:3229205/136‑1 (MQ=255) tcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGa < 1:63738/139‑1 (MQ=255) tcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACGGGA‑GTTGC‑CATGATGAGCGa < 1:3593688/139‑1 (MQ=255) ttATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGaaa < 1:354561/139‑1 (MQ=255) tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGCCTTTTTTCCGACAAATAAAACAAATGGA‑GTTTC‑CCTGATGCGCGCAAg > 1:1422628/1‑139 (MQ=255) tATTTTCGCGTTGATTCAAGAACTGTTAATTAAATATTCACGGTGGCAACAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGAGGTGAAGTTTTTCAAGCAAATACAAAAACAGGA‑GTTGG‑ACTGGTGAACGAAAg > 1:862252/1‑139 (MQ=255) ttttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAAta > 1:1785685/1‑139 (MQ=255) ttttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGta < 1:1767731/139‑1 (MQ=255) ttttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGta < 1:3905763/139‑1 (MQ=255) ttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGtaat < 1:3707772/139‑1 (MQ=255) gcgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCCGACAAATACAAAAAATGGA‑GTTGC‑CATGATGAGCGGAAGgaatact > 1:1057454/1‑137 (MQ=255) gcgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAATACAAAAAATAGA‑GGTGG‑CATTGTTAGGGAAAATAATAAg > 1:3183993/1‑139 (MQ=255) ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAgg < 1:1154526/139‑1 (MQ=255) tCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGc < 1:1386596/139‑1 (MQ=255) cACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATTATGAGCGAAAGTAATAAGCAACAGGCa < 1:3034310/139‑1 (MQ=255) aCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑g < 1:2343222/99‑1 (MQ=255) tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACa < 1:2667585/81‑1 (MQ=255) tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATa < 1:1003426/139‑1 (MQ=255) aaTTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGtt < 1:3601251/139‑1 (MQ=255) tACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGa < 1:89537/106‑1 (MQ=255) tACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGc < 1:2366398/124‑1 (MQ=255) aCATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTgg < 1:2258751/87‑1 (MQ=255) atatTCACGGTGGCAAAAAATATACAACCACATTTTTAGTGGTAGTTTGTGTCGGAAAATTTTTTCATGCCAAAATAAAAAATGGA‑GTTGC‑CCTTATGAAGGGAAGGAATAAACAACAAGCAGAGACTAAATTGGCagg > 1:547/1‑138 (MQ=255) atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACaaaaa > 1:494982/1‑81 (MQ=255) atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGa < 1:666446/103‑1 (MQ=255) atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTT‑TAAAAAAAAAAAAAAACAGGT‑GGTTG‑CATGATGAGGGGAAGTAATAAACAACAAGCAGTTGATAAAGTGACcgaa > 1:3682712/1‑138 (MQ=255) atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAACGGA‑GGTTG‑CATGTTGAACGAAAGTAAAAAGGAAAAAACAAAGAATAAGTGGACaaggg > 1:3598493/1‑135 (MQ=255) atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCCGACAAATACAAAAAATAGA‑AGTGC‑CCTGATTAGCGAAAGGAATAAACAACAGGCAGGGAATAAAGTGAAAgaga > 1:1432473/1‑139 (MQ=255) atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAAAAAAATAAAAAAAATGGA‑GGTGT‑CATGATGAGTGAAAGGAAAAAAGAACAAGGAAGGAATAAGTTTGCAgaga > 1:244643/1‑139 (MQ=255) atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGAGGAATTTTTCAGAAAAATAAAAAAAATTGAGGTTGC‑C‑TGGTGAGCGACAGGAATAAACAAAAGGCAGAGAAAAAAGTGACaggag > 1:2180049/1‑136 (MQ=255) atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGGTTGTGGCGGTGAATTTTTCCAGACa < 1:1362200/69‑1 (MQ=255) ttCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATa < 1:4207829/126‑1 (MQ=255) aCGGTGGCAAAAAATATAAACCCACATTTTTAGGGGTAGTTTGGGGCGGGGAATTTTTTCAGACAAAAAAAAAAACTGGG‑GGTGC‑CCTGATGGGGGAAAAGAAAAAAAAACAGCAAGGGAAAAAGTTAACAGAGATTGt > 1:1813464/1‑139 (MQ=255) tGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAACCGGA‑GTTGC‑CCTGATGAGCGAAAGGAATAAACAACAAGCAATGAATAAATTTACAGAGATTGTCGCt > 1:1800598/1‑139 (MQ=255) ggCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt < 1:3253767/138‑1 (MQ=255) cAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGAGAATTTTTCCAGACAAATACAAAAACTGGA‑GGTTC‑CATGATGAGCGAAAGTAATAAACAAAAAGCAGTGAATAAATTGACaga > 1:2038077/1‑126 (MQ=255) aaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTACCTTTa < 1:1012175/139‑1 (MQ=255) tataAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa < 1:99327/107‑1 (MQ=255) caTTTTTAGTGGTAGTTTGTGGCGGAGAATTTTTTCAAACAAAAAAAAAAAAAGGG‑GTTGCACAGGA‑GGGCGAAAGGAATAAAAAAAAGGGAGGGAAGAAGATGACAAAAGGTGTAGGAAAATTTACCACCATGAtttt > 1:75917/1‑138 (MQ=255) atttttgAGTGGTTGTTGGGGGGGGGAAATTTTTCCAAAAAAAAAAAAAAACGGGA‑GTTGC‑CATGATGAGCGAAAGTAAAAACCACCAGGGAGTAAATAAGTAGACAGAGATTGTCGTAAACTTTACCGCCATGATTTc < 1:3983704/137‑1 (MQ=255) aTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGATAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAgg < 1:843336/89‑1 (MQ=255) aGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTg < 1:1300256/97‑1 (MQ=255) gTGGTAGTTTGTGGCGGTGGATTTTTTCAGACAAAAACAAAAAATGGA‑GGTTT‑CATGGTGTGAGGAAATAATAAAAAACAAGCAGTGAAAAAAATGACAGAGATTGTTGGGCAACTTACAGCCCTGATTTTTACCCGaa > 1:2702712/1‑139 (MQ=255) tttGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGA‑GTTGG‑CCTGGTGGGCGGAAGTAATAAACAAAAAAGAGGGAAAAAGTTGACAGAGAGTGTCGCTAACATTAACGCCATGATTTCTACCCCAAAGGCtga > 1:2413200/1‑139 (MQ=255) tgtgGCGGTGAATTTTTCCAGAAAAATACAAAAACGGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGAAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg < 1:3955962/139‑1 (MQ=255) tggggCGGTGAATTTTTCCAAAAAAAAACAAAAACGGGA‑GTTGC‑CATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg < 1:2944354/136‑1 (MQ=255) gtgGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGA‑GGTGC‑CCTGATGAGCGGAAGGAATAAGAAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCCTGATTTTTTCCCGAATGCCtgatg > 1:772188/1‑138 (MQ=255) ggTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGAAATAAGAAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCCGATGACgtg < 1:1463924/138‑1 (MQ=255) ggTGAATGTTACAATAAAAATAAAAAAACAGGA‑GTTGC‑AAGGATGAGCGAAACTAATAGGCAACGGGCTGTTAAGAGTTTGACAGAGTTTTTCGCTACATTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg < 1:2173944/138‑1 (MQ=255) aaTTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAgg < 1:1409026/63‑1 (MQ=255) aaTTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATaa < 1:1829562/73‑1 (MQ=255) aTTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAGGTTGACAGAGATTGTCGCTATCTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa < 1:240230/138‑1 (MQ=255) aTTTTTCCAGACAAATAAAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa < 1:479163/138‑1 (MQ=255) ttCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAgg < 1:2396082/58‑1 (MQ=255) | AAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGC‑CATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGA > CP009273/3199657‑3199925 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |