| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | NC_002947 | 5,903,164 | G→T | 15.0% | intergenic (‑128/‑140) | PP_5175 ← / → PP_5176 | HlyD family secretion protein/hypothetical protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 5,903,164 | 0 | G | T | 15.0% | 109.3 / 11.1 | 51 | intergenic (‑128/‑140) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (21/22); new base T (3/5); total (24/27) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 7.07e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.91e-01 | |||||||||||
GGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCG > NC_002947/5903020‑5903302 | ggACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGcc < 3:176761/149‑1 (MQ=255) gACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGccc > 5:114253/1‑149 (MQ=255) aCGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCcg > 2:22216/1‑149 (MQ=255) aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGACATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGCGAGCCcgct > 6:275743/1‑146 (MQ=255) tCAACGCCATGCTGGCGCCTTGCTTGGGCCCAAATGATTTGGGGGATGCGACTGTGAGCGTAGTGCAGGGGTCGATAA‑ACCTCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAag < 5:330374/149‑1 (MQ=255) aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGTGAGCCCGCGAaga < 5:226190/148‑1 (MQ=255) aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCTCGCCCGCGAagag < 4:131032/149‑1 (MQ=255) aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCTCGCCCGCGAaga < 7:50155/148‑1 (MQ=255) aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAagag > 6:156144/1‑149 (MQ=255) aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCATCGCGGGCGAGCCCGCGAagag > 2:81406/1‑149 (MQ=255) tCCTTGCTTGTTCAAAATTTATTTGTGGGATGCTACTGTTATCTTAGTTCTGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCTAAGAG‑GCCTCCACAGCCAt < 4:332951/149‑1 (MQ=255) tCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCAt > 3:95037/1‑149 (MQ=255) cttgTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGTCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATc < 3:294196/148‑1 (MQ=255) tgCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCATCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTAt < 1:81406/149‑1 (MQ=255) aaaTGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAGACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGc > 1:81408/1‑149 (MQ=255) aaaTGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGTGCCTCCACAGCCATGT‑ATCAGTATCTGc < 1:22216/149‑1 (MQ=255) tgtgGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGA‑ATCAGTATCTGCCATATCCa < 4:95037/148‑1 (MQ=255) aTGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTAt > 2:48099/1‑130 (MQ=255) aTGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTAt < 1:48099/130‑1 (MQ=255) cGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATc < 6:114253/148‑1 (MQ=255) tgtgAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTATTAGCGGGCGCGCCCGCGCAGAG‑GCCTGCACAGCCATGT‑ATCAGTATATGGCATATGCAGAAACCATCAGGc > 8:89207/1‑148 (MQ=255) aGCGTAGTTCAGGGTTCGATAA‑ACAGCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCGGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAg < 7:25285/105‑1 (MQ=255) gCGTAGTTCAGGTTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGc < 1:196959/149‑1 (MQ=255) gTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATcc < 5:156144/149‑1 (MQ=255) ttCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAg < 4:239637/135‑1 (MQ=255) ttCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAg > 3:239637/1‑135 (MQ=255) taTAA‑ACTTAACTTACGGGGGCCATGCTGGCTTTTTTGTTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCTAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCaa < 1:152204/146‑1 (MQ=255) aTAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTATTAGCGGGCGGGCCCGCGGAGAG‑GGCGCCCCAGCCCAGT‑ATAACTATCTGCCATATGCACGAACCCTCACGCCTCAGGCCTACCCCG‑‑TCCAAccc > 2:316548/1‑148 (MQ=255) aCATCACTGACGTGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTAc > 1:35227/1‑149 (MQ=255) tCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGCGAGCCCGCGAAGAC‑GCCACCACAGCCAAGT‑ATCAGTTTCTGCCATATCCAGAAACCAAACGGCCTC‑GGCCATCCCCCA‑TACAACCCCGACCtt > 6:287738/1‑149 (MQ=255) aCTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATACAGAAAACATCAGGCATA‑GGCCATCCCCGT‑TCCAACCGCTACCatt > 2:252125/1‑148 (MQ=255) aCTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGCGAGCCCGCGCAGAG‑GCCTCCACAGCCAAGG‑ATCAGTATCGGCCATATCCAGAAACCAACCCGCAAC‑GGCCCTCCCCGT‑TCCAACCGCGACCgttg > 2:111507/1‑148 (MQ=255) tGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCAGCCATATCCAGAAACCAACAGGCATC‑GGCCATCCCCGG‑TACAACCGCAACCtttaa > 8:105901/1‑146 (MQ=255) gggCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAg < 7:105901/149‑1 (MQ=255) cATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCaa < 2:81408/149‑1 (MQ=255) aTTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGTATCCAACCGCTACCTTTCACAGGGAGGCTCACATTCaa < 1:252125/149‑1 (MQ=255) ttGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGaa < 5:287738/148‑1 (MQ=255) tGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCaa < 7:69746/136‑1 (MQ=255) tGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCaaa > 3:246181/1‑147 (MQ=255) gCCGCTGCGCGGGCTAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTa < 5:235952/149‑1 (MQ=255) ccTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGTGATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGt > 1:71457/1‑147 (MQ=255) ctctTCGCGGGCTCGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑GCCAACCGCTACCTTTCACAGGGAGGCTCCCATTCAAGGAAGATCAAAATGCAGTTAGc > 7:62438/1‑149 (MQ=255) ccgttCGGGGGCTAGCCCGCTATGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGc < 5:49331/146‑1 (MQ=255) tctTCGCGGGCTCGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGcc > 7:193793/1‑149 (MQ=255) tctTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTc < 3:278241/106‑1 (MQ=255) tctTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTc > 4:278241/1‑106 (MQ=255) gctTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGcc < 4:150935/148‑1 (MQ=255) ttCGCGGGCTCGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTa > 3:51473/1‑144 (MQ=255) ttCGCGGGCTCGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTa < 4:51473/144‑1 (MQ=255) ttCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCg > 8:143564/1‑148 (MQ=255) ttCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTAACTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCg > 5:16963/1‑148 (MQ=255) | GGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAA‑ACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAG‑GCCTCCACAGCCATGT‑ATCAGTATCTGCCATATCCAGAAACCATCAGGCATC‑GGCCATCCCCGT‑TCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCG > NC_002947/5903020‑5903302 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |