| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 5,159 | 0 | G | A | 56.6% | 19.7 / 73.5 | 53 | intergenic (+139/‑75) | thrC/yaaX | threonine synthase/DUF2502 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (23/0); new base A (0/30); total (23/30) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.60e-15 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.71e-11 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATG > NZ_CP009273/5070‑5245 | cTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGgag < 1:229106/90‑1 (MQ=255) gaagaaATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATaacaac > 1:1051452/1‑90 (MQ=255) aaaaaTTAGGAAAAAAAATGACAGGAAAAAAGGAAAAATTCTAAATAAATGCGGTAATTTAGAGATTAGGATTGGGAAAAATAACAAccg < 1:528778/88‑1 (MQ=255) aTTATGGAAAAAAATGAAGGGAAAAAAGGAAAAATTCTAAAAAAAGGCGGTAATTTAGAGATTGGGATGGGGAAAAATAACAACCGCCGt < 1:311411/90‑1 (MQ=255) agaAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATc > 2:1621871/1‑90 (MQ=255) aaaggaaaggAAAAAAGGAAAAATTCAAAAAAAATGCGTTAATTTAGAAATTAGGATGGGGGAAAAAAACACCCGCCGTTCTCATCGAGt < 1:1409295/90‑1 (MQ=255) aaaTGAAAGAAAAAAAGGAAAAATTCTAAAAAAAGGGGGTAATTTAGAGATTAGGTTGGGGGAAAAAAACACCCGCCGTTCTCATCGAGt < 1:43333/90‑1 (MQ=255) aaTGACAGGAAAAAAGGAAAAATTCTAAAAAAAGGGGGTAATTGAGAGTTGGGGTTGGGGGAAAAAAACACCCGCCGTTCTCATCGAGTa < 1:498512/90‑1 (MQ=255) aCAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAAtct > 2:133744/1‑90 (MQ=255) aggaaaaaaggaaaaaTTCTAAAAAAAGGCGGTAACTTAGAGATTAGGATTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTcc < 2:94421/90‑1 (MQ=255) gggAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCg > 1:327634/1‑90 (MQ=255) ggaaaaaaGGAAAAATTCTAAAAAAATGGGGTAACTAAGAGATTAGGATGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCg < 1:139773/87‑1 (MQ=255) ggaaaaaaGGAAAAATTCTAAAAAAATGCGGTAACTTAGAGATTAGGATTGCGGAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCg < 2:660031/87‑1 (MQ=255) aaaaaaGGAAAAATTCTAAAAAAATGCGGTAATTAAGAGATTGGGATGGGGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGa < 1:166822/89‑1 (MQ=255) aaaaaGAAAAATTTCAAAAAAAAGGGGGTAACTTAGAGATTAGGATTGGGGAAAATAACACCCGCCGTTCTCATCGAGTAATCTCCGGat < 1:798234/90‑1 (MQ=255) aaaaaGAAAAAATTCTAAAAAAATGCGGTAACTTAGAGATTAGGATTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGat < 1:90187/90‑1 (MQ=255) aaGGAAAATTTCTAAAAAAATGCGGTAACTTAGAGATTAGGATGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATc < 2:868220/90‑1 (MQ=255) aaGGAAAAATTCTAAATAAATGGGGTAATTTAGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATc < 2:1797221/90‑1 (MQ=255) aaGGAAAAATTCTAAAAAAATGGGTTAATTTAGAGATTGGGTTGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATc < 2:982293/90‑1 (MQ=255) aaGGAAAAATTCAAAAAAAAGGGGGTAACTTAGAGATTGGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATc < 1:533043/90‑1 (MQ=255) agaAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc > 2:1525239/1‑90 (MQ=255) agaAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc > 1:1584549/1‑90 (MQ=255) agaAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc > 2:1651221/1‑90 (MQ=255) gaAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAccc > 2:1089738/1‑90 (MQ=255) tcAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACgg > 1:1519785/1‑90 (MQ=255) aaaaaaTGCGGTAATTTAGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGc < 2:891923/87‑1 (MQ=255) tAAATGCGGTACCTAAGAGATAAGGATTGCGAAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa < 1:860648/90‑1 (MQ=255) tAAATGCGGTAACTTAGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa < 2:636804/90‑1 (MQ=255) aaaaTGGGGTAACTTAGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa < 2:244987/89‑1 (MQ=255) aaaaTGCGTTAATTAAGAGATTGGGTTGGGGGAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa < 1:241534/89‑1 (MQ=255) aaaaTGCGTTAATTAAGAGATAAGGATGGGGAAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa < 1:1525239/89‑1 (MQ=255) aaaaTGCGGTATATTAGAATTTAGGATTGGGAAAAATAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa < 2:1092291/89‑1 (MQ=255) aaaaGGCGATAATTAAGAAATTAGGATGGGGAAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAAAGGGCaa < 1:1651221/89‑1 (MQ=255) aaggCGGAAATTTAGAAATGGGGATGGGGAAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATg < 1:1089738/87‑1 (MQ=255) aaTGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATg > 1:85188/1‑90 (MQ=255) gttAATTTAGACATTGGGTTGGGGGAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaaa < 1:1815805/88‑1 (MQ=255) ggTAATTTAGAGATTAGGATGGGGAAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaaa < 1:1874954/90‑1 (MQ=255) ggTAACTTAGATATGGGGATGGGGAAAAAAAACACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaaa < 1:70668/90‑1 (MQ=255) ggTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaaa > 1:1854972/1‑90 (MQ=255) tAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAg > 2:239485/1‑90 (MQ=255) tAGAGATTAGGTTTGCGAAAAAAAAAACCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTa < 2:769003/90‑1 (MQ=255) aaaTTAGGATGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAAcc < 2:243332/88‑1 (MQ=255) ttAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgt > 2:1819564/1‑90 (MQ=255) tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAAccctgt > 1:1852894/1‑86 (MQ=255) tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg > 1:842829/1‑90 (MQ=255) tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg > 2:1819745/1‑90 (MQ=255) ggATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaa > 2:343167/1‑90 (MQ=255) aTTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa > 2:418990/1‑90 (MQ=255) aTTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa > 2:451081/1‑90 (MQ=255) gCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGa > 2:755260/1‑90 (MQ=255) gCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGa > 1:39690/1‑90 (MQ=255) gCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGa > 2:1118680/1‑90 (MQ=255) gCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGa > 1:1663335/1‑90 (MQ=255) ggAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATg < 1:755260/90‑1 (MQ=255) | CTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATG > NZ_CP009273/5070‑5245 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |