Predicted mutation | |||||||
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evidence | seq id | position | mutation | freq | annotation | gene | description |
RA | NC_002947 | 5,746,488 | G→C | 13.3% | intergenic (+35/+64) | PP_5042 → / ← PP_5043 | hypothetical protein/PhoPQ‑activated pathogenicity‑like protein |
Read alignment evidence... | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | NC_002947 | 5,746,488 | 0 | G | C | 13.3% | 116.2 / 11.1 | 45 | intergenic (+35/+64) | PP_5042/PP_5043 | hypothetical protein/PhoPQ‑activated pathogenicity‑like protein |
Reads supporting (aligned to +/- strand): ref base G (23/16); new base C (3/3); total (26/19) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 6.86e-01 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.43e-01 |
GCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAA > NC_002947/5746348‑5746623 | gCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCt < 4:400505/149‑1 (MQ=255) cTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTc < 4:291869/149‑1 (MQ=255) ccgatctATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGGCGGGCCACGGCCGGGGTATTGCGCCTACAACCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCt < 1:235629/143‑1 (MQ=255) ccATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGTTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGCTCGAtttat < 2:266201/149‑4 (MQ=255) ccATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGCTCGAtttat > 8:170193/1‑146 (MQ=255) ccATTTATGACAAGCGCCCGGATACCTGCCGAAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCtg < 6:145013/149‑1 (MQ=255) cATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGCTCGAtttatg < 7:170193/149‑5 (MQ=255) tGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCt > 2:235629/1‑141 (MQ=255) gACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATg > 7:319888/1‑149 (MQ=255) aCAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGc > 6:121157/1‑149 (MQ=255) gcgcCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAg > 5:236451/1‑149 (MQ=255) ccTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCCAGCTCGGCAtcgc < 6:121103/149‑4 (MQ=255) cTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAg > 7:27054/1‑149 (MQ=255) tGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAg > 4:336049/1‑148 (MQ=255) ccaccCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAAcc > 1:56677/1‑149 (MQ=255) ccccAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCAc > 7:334997/1‑149 (MQ=255) cccAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATAGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCAGTGATCCCAcc > 7:70107/1‑149 (MQ=255) cacggTCGGGCCACGGCGGGGGTATTGCGCCTACAAGCCCAAGGTGGTGGGGGGTTTAGTCTTGCGCCGGGGCATAATTCGCGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTgg < 2:147751/123‑1 (MQ=255) cAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTgg > 1:147751/1‑126 (MQ=255) cAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGCt > 7:287949/1‑101 (MQ=255) cAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGCt < 8:287949/101‑1 (MQ=255) gTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTccc < 8:319888/149‑1 (MQ=255) gggCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCAtt > 2:386711/1‑149 (MQ=255) gCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCAttt > 1:297405/1‑148 (MQ=255) ccACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCgcgggcgg < 2:265406/87‑1 (MQ=255) ccACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCgcgggcgg > 1:265406/1‑87 (MQ=255) ccACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTca < 3:336049/149‑1 (MQ=255) ccACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTca < 2:56677/149‑1 (MQ=255) gTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCgggg > 4:249588/1‑148 (MQ=255) ccTACAAGACACTGGTGGTTGTGGTTTGAGTATGGCGCTGGGGCATAATGCGAGCGCCGGGGGGGGGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCgg < 8:350309/149‑1 (MQ=255) gCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCAc > 7:175940/1‑149 (MQ=255) tggtgtgtGGGCGTTTAGTATTGCGCCGGGGCATAACTCGCGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCAcccccc < 8:334997/142‑1 (MQ=255) ggtTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGAt > 5:381043/1‑149 (MQ=255) gtTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATc < 5:121157/149‑1 (MQ=255) gtTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATc > 2:87059/1‑149 (MQ=255) ttGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATcc > 5:192446/1‑149 (MQ=255) tggggTTGAGGCTGCCGCCGGGCCATAACTCGACAGGCTCGCGGGCGGCGCTCGATTCTGTGGCGATGCTGAGCGTGGCATGAAGCACTTAACCCAGCGCTCCCATTTCAGCCAGCGGGGAAGCTCCTGCAAGCACCCCCCTGATCCg < 8:342836/144‑1 (MQ=255) gCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCtg > 2:31029/1‑149 (MQ=255) gCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCtg > 7:11977/1‑149 (MQ=255) gAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGa > 8:162550/1‑149 (MQ=255) gAGTCTTGCGCCGGGGCACAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCtggtgg > 8:241884/1‑148 (MQ=255) ttGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCt > 2:131717/1‑148 (MQ=255) gcgcAGGTGCTTAATTCGAGCGCCGCGCGGGCGGCGCTGTATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCa < 2:297405/148‑1 (MQ=255) gcCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGa < 6:80898/149‑1 (MQ=255) aTAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGACGAGCTGGGCATGAAGCACTGAACCCCCCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTg > 7:170061/1‑149 (MQ=255) aTCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGc < 1:31029/149‑1 (MQ=255) gAGCGCCGCCCGCGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGTTGGTGGATGCTCAGGATAAGTCTGCGGCaa > 6:419626/1‑148 (MQ=255) | GCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAA > NC_002947/5746348‑5746623 |
Alignment Legend |
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Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |