| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 277,737 | C→A | 13.8% | intergenic (‑43/‑252) | yagA ← / → yagE | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 277,737 | 0 | C | A | 13.8% | 106.7 / 2.2 | 36 | intergenic (‑43/‑252) | yagA/yagE | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| Reads supporting (aligned to +/- strand): ref base C (15/16); new base A (2/3); total (17/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.24e-01 | |||||||||||
TGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACC > CP009273/277492‑277901 | gggggCGGGATGCGCGGGCGGTCCTGCAGGCCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTATGGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGa < 2:624255/269‑1 (MQ=255) gTCCTGAAGACCGGCGGCACCTTCCTGAGCCAAGCGCTGGAGCAACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGAAGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGGCATGGTATCTCCAGCATCCCAGGGACTAAGCGCCTCCATAAACGGGATCTTATACCTTAGTTGTAAGTGTACACCATATCACCCAAAAAGTGTTCAAGATGGCCCCGGACCGTACACCCCACACGGgagca > 2:48667/1‑273 (MQ=255) cggcggCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGCCGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCTAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAAAAGGAACTGCAc > 1:106034/1‑274 (MQ=255) cggcggCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAg > 2:125088/1‑223 (MQ=255) ggcACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGtt < 1:125089/223‑1 (MQ=255) tAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCa > 2:350760/1‑216 (MQ=255) cGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAgg < 1:350765/216‑1 (MQ=255) ggCAGGTGAAATGCCGAAGCTACGGTAGAGGTAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACTTAATGACATGTTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGa < 1:48667/275‑1 (MQ=255) cGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCg > 2:496616/1‑112 (MQ=255) caaaacaaaCTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGAt < 1:55550/227‑1 (MQ=255) caaaacaaaCTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCACGAACa < 1:496624/112‑1 (MQ=255) aTGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCACGaa > 1:578200/1‑90 (MQ=255) cATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCACGAACAAg < 2:578189/90‑1 (MQ=255) gTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTcccc > 1:226019/1‑79 (MQ=255) gTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCg < 2:15993/80‑1 (MQ=255) ctctcGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAAc < 2:226015/79‑1 (MQ=255) cAGGGCATAAGCGACTCCATCAACGGGTTCTTATGCATTAGTTGTAAGTGTCTACCATGTCCCCGAACCAGTGTTCACTATGTCCCCGGACTGTACACACCAAAGGGgaga > 2:21578/1‑111 (MQ=255) gCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAgggg < 1:21578/111‑1 (MQ=255) aTAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCACGAACAAGTGTTc > 2:580259/1‑70 (MQ=255) gCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCACGAACAAGTGTTCACTa < 1:580270/70‑1 (MQ=255) aCTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTggggt > 2:578396/1‑141 (MQ=255) cTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTc > 1:562748/1‑62 (MQ=255) cATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTggggtgtac < 1:578407/142‑6 (MQ=255) aTAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTa < 2:562737/62‑1 (MQ=255) ttCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCACCCTCGCCCCTTTGGGgag > 2:415823/1‑129 (MQ=255) cTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCAGTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGAGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCGAGCTTAAATTTCCCGCTCTCCCTCTTCACTTCCGCtttg > 2:84595/1‑195 (MQ=255) tATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCACCCTCGCCCCTTTGGGGAGAggg < 1:415828/129‑1 (MQ=255) aGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTcc > 2:574793/1‑91 (MQ=255) tgtCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACAccc > 2:619229/1‑52 (MQ=255) tCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCt < 1:574804/91‑1 (MQ=255) tCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGGGGCGAGGGCCGGGGTGAgg > 2:309327/1‑121 (MQ=255) tCTACCATGTCCCCGAACAAGTGTTCACTATGTCACCGGACCGTACACCCCa > 1:450399/1‑52 (MQ=255) cTACAATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGAtt > 1:604504/1‑172 (MQ=255) tACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCcaa < 1:619240/52‑1 (MQ=255) ccATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAgg < 2:450393/52‑1 (MQ=255) ccATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCa < 1:309332/121‑1 (MQ=255) aaTGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTAcc < 2:604493/171‑1 (MQ=255) ccGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTTCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGGGGATAGGGCCGGGGTGAGGGGCAATATGTGATCCAGc > 1:304906/1‑127 (MQ=255) | TGGTGCGGAATGCGCGGGCGGTCCTGAAGACCGGCGGCACCTTCCTGAGCCCAGCGCTGGAGCCACTTGTAGCCGGTGGCAGGTGAAATGCCGAAGCGACGGCAGAGGGAACGGATGTTCGCCCCGTCCTGCGAGGCGAACAAAACAAACTCAGTACGTAATGACATGGTATCTCTCGCATCCCAGGGCATAAGCGACTCCATAAACGGGTTCTTATGCCTTAGTTGTAAGTGTCTACCATGTCCCCGAACAAGTGTTCACTATGTCCCCGGACCGTACACCCCAAAGGGGAGAGGGGACTGCACCGAGCCATCTTTTCCCCCTCGCCCCTTTGGGGAGAGGGCCGGGGTGAGGGGCAATATGTGATCCAGCTTAAATTTCCCGCACTCCCTCTTCCCTTCCGATTTACC > CP009273/277492‑277901 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |