| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_000913_3_vch_pgi | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_vch_pgi | 3,560,455 | 1 | . | G | 95.2% | 57.9 / ‑4.9 | 22 | intergenic (‑2/+1) | glpR/glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| Reads supporting (aligned to +/- strand): ref base . (0/1); major base G (10/10); minor base A (1/0); total (11/11) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01 | |||||||||||
GATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATA > NC_000913_3_vch_pgi/3560310‑3560579 | gttatGGATAAACAGCGGCGGGCCATTGGGGATTTTCTTCGCGCGTTGGCGGGGGAGGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGcgca < 2:80341/147‑4 (MQ=255) atatCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGT‑CTGGGTGCCCTTGAGATCGTGGGACTGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ACGATCGcgcag > 2:196952/1‑145 (MQ=255) atatCGATAAACAGCGTCGAGCCATAGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGG‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGAGGGcgcag > 2:196443/1‑145 (MQ=255) gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCa > 2:163392/1‑149 (MQ=255) aaCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGtt < 1:163392/149‑1 (MQ=255) aTTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑Ag < 1:27012/149‑1 (MQ=255) gtGCTCCGCCACGTTGCGGGCGAGGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGt < 2:254557/148‑1 (MQ=255) gCTCCGCCACTTTGCGGGCGATGCGCTCTTTTT‑TTAGCTGCCCGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTcg > 1:240407/1‑149 (MQ=255) tCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATAGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCACACGATCAGGCTTTGCTCCGACAGCTCAGTG‑AGGTcgcg > 2:259967/1‑149 (MQ=255) cGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCgcggc < 1:235224/149‑1 (MQ=255) tttGCGGGCGATGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGACACAGGTTTTGCTCCGCCACCTCAGTG‑AGGGCGCGGCGACTAg > 2:234970/1‑149 (MQ=255) ggCGATGCGCTCTTTTTCTCCGGT‑CTGGGCGGCCCTGCGATCGTGCCACGGCTTGTTAACCAAGTTGATTGGCATCGCCGAACCGCCTGTGTTTCG‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCg < 1:238904/149‑1 (MQ=255) cgcTCCTTTTCTTCGGG‑CTGCGTGGCCTTGCGGTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGAc < 1:88169/149‑1 (MQ=255) ttcGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct > 2:153910/1‑149 (MQ=255) ggggttGGGTGGCTGTGCGGGCGTGCCACGGCGAGGTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGctct < 2:162040/144‑1 (MQ=255) ggT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGTCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTa < 1:212656/149‑1 (MQ=255) gCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGGTCAGGTTTTGCTCCGCCGGCTCATTG‑AGGTCGCGGCGAGTAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTc > 2:145040/1‑149 (MQ=255) ttGCGATCGTGCCCCGGCGGGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGt > 2:200393/1‑149 (MQ=255) cGATCGTGCCGCGGCGTGTTGACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACt < 2:182582/149‑1 (MQ=255) aTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGGACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCAGCA‑CGCAGCGCAGATTTCGGCGATTCGTATGCTGGCTGACGGAGACCTGCTCTGCCAGCTCTTCGGTACTGa < 2:311430/149‑1 (MQ=255) aTCGCGCCACGGGGTGGTAACCGCACTGGAAGGCAGCGGCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCGCCGCCAGCTCATTG‑AGGGCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGa < 2:88535/149‑1 (MQ=255) tCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGAc > 2:205171/1‑149 (MQ=255) ccACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTGTGCTCCGCCAGCTCCTTG‑AGGTCGCGGCGAATAGTCGGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAc > 2:179330/1‑149 (MQ=255) aaCCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGATTaa > 1:108738/1‑149 (MQ=255) gCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAAAAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACAAGTTCGctcata > 1:109981/1‑149 (MQ=255) | GATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGT‑CTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTG‑AGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATA > NC_000913_3_vch_pgi/3560310‑3560579 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |