| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_000913 | 2,406,097 | (T)5→6 | coding (545/939 nt) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,406,092 | 1 | . | T | 78.4% | 141.3 / 33.5 | 51 | coding (550/939 nt) | lrhA | transcriptional repressor of flagellar, motility and chemotaxis genes |
| Reads supporting (aligned to +/- strand): ref base . (5/6); new base T (22/18); total (27/24) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 7.36e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01 | |||||||||||
CCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCATA > NC_000913/2405960‑2406225 | ccGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTAATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGCGGGATCGGCTCGCC‑ttttt < 1:6426/138‑1 (MQ=255)ccGCACGAACGCCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTAATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑ttttt > 2:6426/1‑138 (MQ=255) cACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑ttttttgca > 1:339027/1‑135 (MQ=255) cACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGACCGGCTCGCC‑ttttttgca < 2:397061/139‑5 (MQ=255) cGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAat < 1:572442/139‑1 (MQ=255) gAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCg < 2:339027/139‑1 (MQ=255) cGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTgcg < 1:643612/139‑1 (MQ=255) gTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTgcg < 1:652041/139‑1 (MQ=255) aTAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAgtg < 2:564150/139‑1 (MQ=255) gTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATACGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGa > 2:237381/1‑139 (MQ=255) ttattaAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAgtg > 1:314949/1‑111 (MQ=255) ttattaAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAgtg < 2:314949/111‑1 (MQ=255) taAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATACGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTaaa < 1:237381/139‑1 (MQ=255) cGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGa < 2:381662/139‑1 (MQ=255) ccAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAg > 1:157091/1‑139 (MQ=255) ccAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAg > 2:530004/1‑139 (MQ=255) cAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAgg < 2:157091/139‑1 (MQ=255) tatCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATggg > 1:381165/1‑139 (MQ=255) aaaCGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTAc > 1:241628/1‑139 (MQ=255) ggCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTg < 1:79546/64‑1 (MQ=255) ggCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTg > 2:79546/1‑64 (MQ=255) gCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCaa > 2:457475/1‑139 (MQ=255) gCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCaa > 1:570219/1‑139 (MQ=255) catcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGtt > 2:243825/1‑123 (MQ=255) catcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGtt < 1:243825/123‑1 (MQ=255) atcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTgcg > 2:410163/1‑56 (MQ=255) atcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTgcg < 1:410163/56‑1 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAg < 1:271437/76‑1 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAg > 2:271437/1‑76 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTc < 1:238010/88‑1 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTc > 2:238010/1‑88 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTcc > 1:682444/1‑139 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGtt > 1:65729/1‑86 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGtt < 2:65729/86‑1 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACg > 1:363538/1‑100 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACg < 2:363538/100‑1 (MQ=255) tcCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCt > 1:581487/1‑139 (MQ=255) gCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATc < 2:569756/123‑1 (MQ=255) gCAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATc > 1:569756/1‑123 (MQ=255) cAATACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGATGATGGGTGGTTACCATCAAATCCAGTTCCTGGGa > 1:458451/1‑139 (MQ=255) aaTACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGAt < 1:530004/139‑1 (MQ=255) aTACAAGAGGGATCGGCGCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGAAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTc < 2:404813/139‑1 (MQ=255) tACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCa < 2:574230/126‑1 (MQ=255) tACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCa > 1:574230/1‑126 (MQ=255) tACAAGAGGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTc > 2:336023/1‑139 (MQ=255) agGGATCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCAt < 2:241628/139‑1 (MQ=255) aTCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCt > 2:564547/1‑139 (MQ=255) aTCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCt > 2:626488/1‑139 (MQ=255) aTCGGCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCt > 2:182098/1‑139 (MQ=255) aTCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTg > 2:434170/1‑139 (MQ=255) aTCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTg < 1:434170/139‑1 (MQ=255) ggCTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGcc > 1:190309/1‑139 (MQ=255) cTCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCat > 1:419952/1‑139 (MQ=255) tCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCata < 2:419952/139‑1 (MQ=255) tCGCCTTTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCata < 1:332414/139‑1 (MQ=255) | CCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAGGGATCGGCTCGCC‑TTTTTGCAATATGTATTCCGCTGCGCAGTACCAGTGTGTTGGCGAGGTACGCAGGTTCAATGCCTTAAACGCTGAAGGACGATGGGTGGTTACCATCAAATCCACTTCCTGGGATTCCAGCATTTCTGCCATA > NC_000913/2405960‑2406225 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |