| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 5,922,204 | 0 | A | C | 57.7% | ‑5.3 / 11.3 | 26 | D271A (GAC→GCC) | PP_5190 | type II secretion system protein |
| Reads supporting (aligned to +/- strand): ref base A (2/9); new base C (2/13); total (4/22) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.57e-01 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CCGTATCGATGGCCTGCTGCACACCGTCTACGCCTTCCCCGCCGGGGTCACCCTGGCCCTCGTCAGCCGCCTGAAACACCTGGGCCGCAT‑GGAC‑GTTGCAGAGAAGCGC‑CGGCC‑GCAGGACGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGACCCGCACCAGTTGCAAGAGGGCTTCGACC > NC_002947/5922085‑5922335 | ccGTATCGATGGCCTGCTGCACACCGTCTACGCCTTCCCCGCCGGGGTCACCCTGGCCCTCGTCAGCCGCCTGAAACACCTGGGCCGCAT‑GGAC‑GTTGCAGAGAAGCGG‑CGGGC‑CCCGCACCGCCCGC‑GGCAAAgc > 1:2616547/1‑136 (MQ=255) tCGAGGGCCGGCTCCACACCGCCACCGCCTCCCCCGCCGGGGCCCCCCGGGCCCTCGCCCCCCGCCTCAAACCCCTGGGCCGCAT‑GGAC‑GTGGCAGAGACGCGC‑CGGCC‑GCAGGACGGCCGGC‑TGCAAAGCCGCCt < 2:470338/136‑1 (MQ=255) ctgctgCACACCGTCTACGCCTTCCCCGCCGGGGTCACCCTGGCCCTCGTCAGCCGCCTGAAACACCTGGGCCGCAT‑GGAC‑GTTGCAGAGAAGCGG‑CCGGC‑GCCGGCCGGCCCGC‑CGCCAACCCCCCCAccccggg > 2:3071880/1‑132 (MQ=255) ctgcACACCGTCTACGCCTTCCCCGCCGGGGTCACCCTGGCCCTCGTCAGCCGCCTGAAACACCTGGGCCGCAT‑GGAC‑GTTGCAGAGAAGCGG‑CGGCC‑GCCGGCCCGCCCGCGGGCAAACCCCCCAACCCgcgggg > 1:1239387/1‑131 (MQ=255) ctccaccCCGTCACCGCCTGCCCCGCCGGGGTCACCCGGGCCCTCGCCCGCCGCCTCAAACCCCTGGGCCGC‑T‑GGCCGGTCGCTGACACGCGC‑CGGCC‑GCAGGCGGGCCGGC‑TGCAAAGCCGCCTACCCGgtggtg < 2:2389585/133‑1 (MQ=255) ctccGCCTCCCCCGCGGGGGCCCCCGGCCCCCGCGCCCGCCCCCTCAACCACGGGGGCCG‑AT‑GGGCGGTTCCAGCGACGCGC‑CGCCC‑GCAGGCGGCCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAg < 2:1026025/133‑1 (MQ=255) cacccccTCCCCCGCCGGGGACACCCGGCCCCTCGCCCCCCCCCTCAAACCCGGGGCCCGCTT‑GGCG‑GTTGACCAGACCCGC‑CGGCC‑CCCGGCCGCCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAg < 2:485049/131‑1 (MQ=255) cTACGCCTTCCCCGCCGGGGTCACCCTGGCCCTCGTCAGCCGCCTGAAACACCTGGGCCGCAT‑GGAC‑GTTGCAGAGAAGCGC‑CCGCC‑GCAGGACGGCCCGC‑AGCAAAACCGCCAACCCCCGGGTGGGGGAGTgggg > 2:3102616/1‑134 (MQ=255) cTACGCCTTCCCCGCCGGGGTCACCCTGACCCTCGTCAGCCGCCTGAAACACCTGGGCCGCAT‑GGAC‑GTTGCAGAGAAGCGC‑CGGCC‑ACAGGACGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAg < 1:45924/136‑1 (MQ=255) ccGCCTCCCCCGCGGGGGCCCCCCGGCCCCGCGCCCGCCGCCTCAACCCCGGGGGCCCCTG‑GCCC‑GTCGCACCTACGCCC‑CGCCC‑CCAGCACGCCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCt < 2:261224/135‑1 (MQ=255) ttCCCCGCGGGGGTCACCCTGGCCCTCGTCAGCCCCCTCAACCACCTGGGCCGAAT‑GTAC‑GTTCCAGATAAGCGC‑CGGCC‑GCAGGACGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGc < 2:2598488/136‑1 (MQ=255) ccccccGCCGGGTTCACCCTGCCCCGCGGCCCCCGCCTCAACCCCCTGGCCCGCAT‑GGAC‑GTTCCAGATACCCGC‑CGGCC‑GCCGGAGGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGc < 2:350710/134‑1 (MQ=255) ggccgGGGTCCCCCGGCCCCGCCGCCGCCGCATCACACACGTGGGCCGCTT‑CGAG‑TGTCCACAG‑ACCGCGCGCCC‑GCAGCACGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCg < 2:254672/135‑1 (MQ=255) cgcggGGGCCCCCCGGCCCCTCGTCCCCCGCCTTAAACACCTGGCCCGCAT‑GGAC‑GTTGCAGACACGCGC‑CGGCC‑GCAGGACGCCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCg < 2:1239387/136‑1 (MQ=255) ccggggggTCCCCCGGGCCCGCGTCCGCCGCCT‑CAACCCCGGGGCCCCCTGGGTG‑GTTCCAGACACGC‑C‑CGGCCGGCCGCCGGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCg < 2:1750804/132‑1 (MQ=255) gccgGGGTCCCCCGGCCCCTCGCCCGCCGCCTCAACCCCCGGGGCCGCAG‑GGAC‑GTTGCAGAGACGCGC‑CGGCC‑GCAGGCCGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGa < 1:4214908/136‑1 (MQ=255) cTCGTCAGCCGCCTGAAACACGTGGGCCGCAT‑GGAC‑GTTGCAGAGAAGCGC‑CGGCC‑GCAGGACGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTg < 2:1820213/136‑1 (MQ=255) aaCACCTGGGCCTCTG‑GGCG‑GTGGCAGACCCGCGC‑CGGCC‑GCTGGCGGGCCGGC‑TGCTAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGtt < 2:2115882/136‑1 (MQ=255) ggggCCGCAG‑GGAC‑GTTGCACCGACGCGC‑CGCCC‑GCAGGCCGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCt < 1:3102616/135‑1 (MQ=255) ggccc‑GTTGCAGACACGCGC‑CGGCC‑GCCGGCGGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGAccc < 2:2355628/132‑1 (MQ=255) tttGCAGTCACGCGG‑CGGGC‑GCTGGCGGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGATGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGACCCGCAcc < 1:4390771/135‑1 (MQ=255) cgcgc‑CGGCC‑GCTGGCCGCCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGACCCGCACCAGTTGCAaga < 1:1478657/135‑1 (MQ=255) ggcc‑gccggccgccCGGC‑TGCAAAGCCGCCTACCCGGTGGGGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGACCCGCACCAGTTGCAAGAGGGCtt < 1:2885689/136‑1 (MQ=255) ggcc‑gCCGGCCGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGACCCGCACCAGTTGCAAGAGGGCtt < 2:3201947/136‑1 (MQ=255) gccc‑gCAGGAGGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGACCCGCACCAGTTGCAAGAGGGCtt < 2:2897542/134‑1 (MQ=255) cAGGCCGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGACCCGCACCAGTTGCAAGAGGGCTTCGAcc < 2:1598804/136‑1 (MQ=255) cAGGCCGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGACCCGCACCAGTTGCAAGAGGGCTTCGAcc < 1:4333100/136‑1 (MQ=255) | CCGTATCGATGGCCTGCTGCACACCGTCTACGCCTTCCCCGCCGGGGTCACCCTGGCCCTCGTCAGCCGCCTGAAACACCTGGGCCGCAT‑GGAC‑GTTGCAGAGAAGCGC‑CGGCC‑GCAGGACGGCCGGC‑TGCAAAGCCGCCTACCCGGTGGTGGCGAAGTGGAGCTGCGGCTTTCGACCCTGCCCACCCCATTTGGCGAGAAACTGGTGTTGCGCCTGTTCGACCCGCACCAGTTGCAAGAGGGCTTCGACC > NC_002947/5922085‑5922335 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |