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_pae_tpiA | 4,159,076 | 0 | T | A | 66.1% | 83.6 / 63.6 | 62 | L224Q (CTG→CAG) | oxyR | oxidative and nitrosative stress transcriptional regulator |
| * | NC_000913_3_pae_tpiA | 4,110,974 | 0 | C | A | 57.1% | ‑2.9 / 77.2 | 50 | intergenic (+289/+557) | cdh/yiiQ | CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein |
| * | NC_000913_3_pae_tpiA | 3,815,801 | 0 | A | . | 46.2% | 165.1 / 157.2 | 80 | intergenic (‑33/+33) | pyrE/rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| * | NC_000913_3_pae_tpiA | 3,440,923 | 0 | C | T | 33.7% | 117.9 / 92.8 | 104 | G36D (GGC→GAC) | rpoA | RNA polymerase, alpha subunit |
| * | NC_000913_3_pae_tpiA | 4,158,703 | 0 | A | G | 33.3% | 75.9 / 55.5 | 64 | T100A (ACA→GCA) | oxyR | oxidative and nitrosative stress transcriptional regulator |
| * | NC_000913_3_pae_tpiA | 4,295,976 | 0 | C | T | 30.8% | 117.4 / 78.7 | 91 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_pae_tpiA | 4,520,416 | 0 | A | . | 23.5% | 242.2 / 75.5 | 85 | intergenic (‑176/+171) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| * | NC_000913_3_pae_tpiA | 4,520,420 | 1 | . | T | 22.7% | 230.4 / 94.0 | 88 | intergenic (‑180/+167) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| * | NC_000913_3_pae_tpiA | 4,366,770 | 0 | T | G | 21.8% | 161.6 / 54.7 | 78 | intergenic (‑81/+37) | dcuA/aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| * | NC_000913_3_pae_tpiA | 4,366,771 | 0 | C | A | 21.8% | 191.9 / 47.5 | 78 | intergenic (‑82/+36) | dcuA/aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| * | NC_000913_3_pae_tpiA | 3,781,051 | 0 | C | G | 20.0% | 183.3 / 40.4 | 75 | intergenic (+34/‑164) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| Marginal new junction evidence (lowest skew 10 of 347 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | = 382205 | NA (NA) | 26 (0.340) | 24/244 | 3.1 | NA | coding (532/906 nt) | insD1 | IS2 transposase TnpB |
| ? | NC_000913_3_pae_tpiA | = 382224 | NA (NA) | coding (551/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | NC_000913_3_pae_tpiA | 59280 = | 81 (1.040) | 22 (0.330) | 20/212 | 3.2 | 24.9% | intergenic (+1/+407) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| ? | NC_000913_3_pae_tpiA | 59320 = | 63 (0.940) | intergenic (+41/+367) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent | |||||
| * | ? | NC_000913_3_pae_tpiA | = 225895 | NA (NA) | 27 (0.370) | 21/232 | 3.4 | NA | noncoding (137/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_tpiA | = 225899 | NA (NA) | noncoding (141/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 3946053 | 3 (0.040) | 21 (0.280) | 17/238 | 4.3 | 87.9% | noncoding (2350/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_pae_tpiA | = 3946069 | NA (NA) | noncoding (2366/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 228108 | NA (NA) | 21 (0.280) | 17/238 | 4.3 | NA | noncoding (2350/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_tpiA | = 228124 | NA (NA) | noncoding (2366/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1755691 | 43 (0.550) | 40 (0.520) | 17/244 | 4.5 | 48.4% | intergenic (‑550/‑7) | ydhZ/pykF | uncharacterized protein/pyruvate kinase I |
| ? | NC_000913_3_pae_tpiA | = 2290112 | NA (NA) | intergenic (‑31/+2) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913_3_pae_tpiA | = 4168257 | 49 (0.630) | 15 (0.210) | 14/226 | 4.8 | 29.1% | intergenic (+141/‑31) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu |
| ? | NC_000913_3_pae_tpiA | = 4168279 | 28 (0.390) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913_3_pae_tpiA | 2731569 = | 96 (1.230) | 18 (0.250) | 14/224 | 4.8 | 17.0% | intergenic (‑412/+31) | rrsG/clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| ? | NC_000913_3_pae_tpiA | 2731595 = | 88 (1.240) | intergenic (‑438/+5) | rrsG/clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone | |||||
| * | ? | NC_000913_3_pae_tpiA | 2729443 = | 38 (0.490) | 15 (0.210) | 14/226 | 4.8 | 27.3% | noncoding (2/76 nt) | gltW | tRNA‑Glu |
| ? | NC_000913_3_pae_tpiA | = 4168247 | 45 (0.630) | intergenic (+131/‑41) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913_3_pae_tpiA | 2700550 = | 100 (1.280) | 16 (0.240) | 12/208 | 4.9 | 15.7% | noncoding (31/77 nt) | ohsC | sRNA antisense regulator of shoB toxin |
| ? | NC_000913_3_pae_tpiA | 2700601 = | 87 (1.320) | intergenic (+5/+17) | ohsC/acpS | sRNA antisense regulator of shoB toxin/holo‑[acyl‑carrier‑protein] synthase 1 | |||||