Predicted mutation | ||||||
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evidence | seq id | position | mutation | annotation | gene | description |
RA | CP009974 | 1,920,754 | 1 bp→TTT | intergenic (‑383/+172) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
Read alignment evidence... | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | CP009974 | 1,920,753 | 1 | . | T | 86.7% | 11.7 / 10.6 | 30 | intergenic (‑382/+173) | RPPX_08560/RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
Reads supporting (aligned to +/- strand): ref base . (1/3); new base T (11/15); total (12/18) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 6.32e-01 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01 | |||||||||||
* | CP009974 | 1,920,753 | 2 | . | T | 86.7% | 11.7 / 10.6 | 30 | intergenic (‑382/+173) | RPPX_08560/RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
Reads supporting (aligned to +/- strand): ref base . (1/3); new base T (11/15); total (12/18) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 6.32e-01 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
* | CP009974 | 1,920,754 | 0 | A | T | 100.0% | 14.0 / NA | 30 | intergenic (‑383/+172) | RPPX_08560/RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (12/18); total (12/18) |
CTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTTGATCGTAGCCCTTACAGC‑‑A‑‑CCTTCCGAATCGTCTAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCA > CP009974/1920691‑1920863 ||||| cTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TACCTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgag < 1:2243879/151‑1 (MQ=11) ttGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgaga > 2:4716883/1‑151 (MQ=2) ttGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgaga < 1:3606830/151‑1 (MQ=2) ggAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGACGTGGGGCGCATTATACGGGGATTCGAGAgg > 2:4451016/1‑151 (MQ=2) ggAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAgg < 2:1026015/151‑1 (MQ=2) ggAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAgg < 2:3060508/151‑1 (MQ=2) gAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTTGAGAggg > 1:2175135/1‑151 (MQ=2) gAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATGATAAGGGGATTGGAGCggg > 1:2175116/1‑151 (MQ=2) aGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCg > 1:974192/1‑151 (MQ=2) aGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCg < 1:1857849/151‑1 (MQ=11) gcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCa > 2:4412377/1‑151 (MQ=2) gcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCa < 2:1156168/151‑1 (MQ=2) tGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTCG‑CTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAc < 2:923169/151‑1 (MQ=2) gTCCACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAcc < 2:1789953/151‑1 (MQ=2) cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt > 1:4597702/1‑151 (MQ=2) cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt < 2:1009439/151‑1 (MQ=2) cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt > 2:4650512/1‑151 (MQ=2) aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TATCTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt < 2:3484699/151‑1 (MQ=2) aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt < 1:714560/151‑1 (MQ=2) aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt < 1:2547308/151‑1 (MQ=2) aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt < 2:461927/151‑1 (MQ=11) aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt < 2:5227266/151‑1 (MQ=2) ccATCTTCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTaa < 1:4357038/151‑1 (MQ=2) ccATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTaa > 1:972799/1‑151 (MQ=2) tcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAttt < 2:2474804/151‑1 (MQ=2) tcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAttt > 1:4022223/1‑151 (MQ=2) tcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAttt < 2:3429108/151‑1 (MQ=2) catcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTc < 1:415163/151‑1 (MQ=2) catcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTc > 1:5039975/1‑151 (MQ=2) atcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGCTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATCATAACGCGATTCGCTATGGCGTCAACCTTTAATTTCa > 2:3751597/1‑151 (MQ=2) ||||| CTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTTGATCGTAGCCCTTACAGC‑‑A‑‑CCTTCCGAATCGTCTAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCA > CP009974/1920691‑1920863 |
Alignment Legend |
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Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |