mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_vch_pgi | 526,792 | 0 | A | C | 44.7% | 17.0 / 28.1 | 40 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_vch_pgi | 526,796 | 0 | C | G | 44.4% | 20.2 / 34.0 | 37 | A1179G (GCG→GGG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_vch_pgi | 526,800 | 0 | A | G | 40.0% | 28.9 / 20.8 | 36 | E1180E (GAA→GAG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_vch_pgi | 860,157 | 0 | C | T | 40.0% | 1.1 / 13.1 | 15 | intergenic (‑129/+17) | ybiV/ybiW | sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase |
| * | NC_000913_3_vch_pgi | 860,151 | 0 | A | G | 37.5% | 3.6 / 11.7 | 16 | intergenic (‑123/+23) | ybiV/ybiW | sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase |
| * | NC_000913_3_vch_pgi | 860,154 | 0 | A | T | 37.5% | 4.5 / 14.5 | 16 | intergenic (‑126/+20) | ybiV/ybiW | sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase |
| * | NC_000913_3_vch_pgi | 4,296,063 | 0 | C | T | 28.6% | 37.9 / 12.6 | 29 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_vch_pgi | = 1636407 | 20 (0.900) | 4 (0.200) | 4/252 | 2.3 | 17.9% | intergenic (‑40/‑349) | nohQ/ynfO | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage |
| ? | NC_000913_3_vch_pgi | = 1636432 | 19 (0.960) | intergenic (‑65/‑324) | nohQ/ynfO | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage | |||||
| * | ? | NC_000913_3_vch_pgi | 696399 = | 18 (0.810) | 4 (0.200) | 4/262 | 2.4 | 19.2% | intergenic (+123/+31) | ubiF/glnX | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln |
| ? | NC_000913_3_vch_pgi | 696425 = | 17 (0.830) | intergenic (+149/+5) | ubiF/glnX | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln | |||||
| * | ? | NC_000913_3_vch_pgi | 1487376 = | 23 (1.040) | 4 (0.190) | 4/272 | 2.5 | 16.0% | coding (142/801 nt) | ydcF | DUF218 superfamily protein, SAM‑binding |
| ? | NC_000913_3_vch_pgi | 1487398 = | 20 (0.940) | coding (164/801 nt) | ydcF | DUF218 superfamily protein, SAM‑binding | |||||
| * | ? | NC_000913_3_vch_pgi | 111593 = | 21 (0.950) | 4 (0.190) | 4/270 | 2.5 | 15.4% | noncoding (164/200 nt) | RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site |
| ? | NC_000913_3_vch_pgi | 111626 = | 24 (1.140) | noncoding (197/200 nt) | RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_vch_pgi | = 3499063 | 19 (0.860) | 4 (0.180) | 4/280 | 2.6 | 17.1% | coding (1236/1374 nt) | cysG | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase |
| ? | NC_000913_3_vch_pgi | = 3499086 | 20 (0.910) | coding (1259/1374 nt) | cysG | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase | |||||
| * | ? | NC_000913_3_vch_pgi | = 2958506 | 28 (1.260) | 3 (0.140) | 3/274 | 2.9 | 9.5% | coding (379/2889 nt) | ptrA | protease III |
| ? | NC_000913_3_vch_pgi | = 2958511 | 30 (1.400) | coding (374/2889 nt) | ptrA | protease III | |||||
| * | ? | NC_000913_3_vch_pgi | = 2729634 | 15 (0.680) | 3 (0.140) | 3/274 | 2.9 | 19.7% | noncoding (1524/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_vch_pgi | 4209658 = | 10 (0.470) | noncoding (1512/1542 nt) | rrsE | 16S ribosomal RNA of rrnE operon | |||||
| * | ? | NC_000913_3_vch_pgi | = 1872229 | 23 (1.040) | 3 (0.140) | 3/270 | 2.9 | 12.0% | coding (189/1491 nt) | yeaJ | putative diguanylate cyclase |
| ? | NC_000913_3_vch_pgi | = 1872232 | 22 (1.040) | coding (192/1491 nt) | yeaJ | putative diguanylate cyclase | |||||
| * | ? | NC_000913_3_vch_pgi | 1429011 = | 30 (1.350) | 3 (0.140) | 3/268 | 2.9 | 9.5% | intergenic (+27/‑38) | lomR/stfR | pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein |
| ? | NC_000913_3_vch_pgi | 1429033 = | 29 (1.380) | intergenic (+49/‑16) | lomR/stfR | pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein | |||||
| * | ? | NC_000913_3_vch_pgi | 724063 = | 23 (1.040) | 3 (0.140) | 3/268 | 2.9 | 12.6% | coding (352/2685 nt) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| ? | NC_000913_3_vch_pgi | 724085 = | 20 (0.950) | coding (330/2685 nt) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein | |||||