| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 3,657,830 | C→A | 13.8% | R50L (CGA→CTA) | gadW ← | transcriptional activator of gadA and gadBC; repressor of gadX |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 3,657,830 | 0 | C | A | 13.8% | 80.9 / 4.6 | 29 | R50L (CGA→CTA) | gadW | transcriptional activator of gadA and gadBC; repressor of gadX |
| Reads supporting (aligned to +/- strand): ref base C (13/12); new base A (2/2); total (15/14) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.63e-01 | |||||||||||
TGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAGCAGACATGAGTCATGATTATCCCTTATATTTCATACTGCGATTATTTCAATTTCAGTATACTAATGAAATGATGCCAGACTGTTTCTTAGCGCAAAAACTGCCAGATTTGGTAGGACCAAAATTTATC > CP009273/3657585‑3658092 | tGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGTTCTTTGCTGTGTAAGCATAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTATCAGCTCATCGATATCCAGTCGTCTCGTATCCGATGAACAAAACGCaaaa > 1:268830/1‑275 (MQ=255) aGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACACAAAATCATCTGCCAAAttttt > 1:200460/1‑275 (MQ=255) tttttAAGANAAAAACTCGATACACATGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCcag < 2:200453/272‑1 (MQ=255) tATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATATTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAACCGCAAAATCGTCTGCCAAATTTTTCTCcagcagc > 1:251959/1‑275 (MQ=255) aaaaCATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAgtcgt < 1:196599/215‑1 (MQ=255) aaaaATAGAGAAAGAGGAAAGGTAGAGCATATGGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAAGCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATAc < 2:367593/275‑1 (MQ=255) tGAATTTACACAGGATTCATTGAAGCTATCAAAAATCGGCGTCACCAGCGGTATGGGGGATGACTGGTTAATGAACAAACGGTCTTTGCTGTGTAACACTAAAGTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAACCTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGa < 1:57075/275‑1 (MQ=255) ccctGGATTTTTTGAAGCTATCAAAAATAGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAacg < 1:36974/274‑1 (MQ=255) gCCGTCAACAGCGGCATTGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCATACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATAGTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAGCAGACATGAGt < 1:312311/275‑1 (MQ=255) ccGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGATGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCt > 1:180370/1‑164 (MQ=255) cACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCa < 2:180363/164‑1 (MQ=255) gACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCAc > 1:267580/1‑236 (MQ=255) gTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGATGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTGGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCGAGCAGGAGAATACTCTCGTTATGCAGAGATATTTTTTGCTGTTCAAGATAAATAGCGAATGAACGAGGAATGAGGATCACCAAGCAAACATGAGTCATGATAATACCTTATATTTCATACTgag > 1:269667/1‑273 (MQ=255) ttaattaaTAAGTGGTTTTTGATTNGTAACCCTCAATTGCGTGGTAACTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAGCAGACATGAGTCATGATTATCCCTTATATTTCATACTGCGa < 2:307027/275‑1 (MQ=255) gtgtAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGc > 2:421577/1‑151 (MQ=255) gtAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTAGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAAttttt > 1:234611/1‑121 (MQ=255) aaCCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCg < 1:421592/151‑1 (MQ=255) cccTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAGCAGACATGAGTCATGAtt < 2:174441/223‑1 (MQ=255) cccTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTAGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTcc < 2:234602/121‑1 (MQ=255) aaTTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAAttttt > 1:151596/1‑112 (MQ=255) gCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAACACGCAAAATCGTCTGCCAAATTTTTCTcc < 2:151593/112‑1 (MQ=255) cGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAGCa > 2:432281/1‑197 (MQ=255) gTAGCTTACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCAGCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAGCAGACa < 1:432296/197‑1 (MQ=255) atatTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGaa > 1:147582/1‑155 (MQ=255) tttGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGaa < 2:147579/155‑1 (MQ=255) gtaaTGGCAAACTGTCAGCTCATCGATATCCAGTAGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAacg > 2:70956/1‑150 (MQ=255) tGGCAAACTGTCAGCTCATCGATATCCAGTAGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAAcgacga < 1:70956/150‑1 (MQ=255) aaCTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAGCAGACATGAGTCATGATTATCCCTTATATTTCATACTGCGATTATTTCAATTTCAGTATACTAATAAAATGATGCCAGACTGTTTCTTATTGCAAAAACTGCCAGATTTggaaag > 2:176586/1‑271 (MQ=255) cGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTATGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAGCAGACATGAGTAATGATTATCCATTATATTTCATACTTCGATTATTTCAATTTCAGTATAATAATGAAATGATGCCAGACTGTTTCTTAGCGCAAAAACTGCAAAAATTATAAGGACCAACATTTATc > 1:210618/1‑274 (MQ=255) tCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCAc > 1:192871/1‑137 (MQ=255) gtcgtcGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAg < 2:192864/137‑1 (MQ=255) | TGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCGTCTGCCAAATTTTTCTCCAGCAGCAGAATACTCTCGTTATGCAGCGATATTTTTTGCTGTTCATGATAAATATCGAATGAACGACGAATGAGGATCACCGAGCAGACATGAGTCATGATTATCCCTTATATTTCATACTGCGATTATTTCAATTTCAGTATACTAATGAAATGATGCCAGACTGTTTCTTAGCGCAAAAACTGCCAGATTTGGTAGGACCAAAATTTATC > CP009273/3657585‑3658092 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |