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 | 1,399,978 | 1 | . | C | 51.8% | inf / inf | 276 | coding (259/516 nt) | ogt | methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| * | NC_000913 | 2,021,636 | 2 | . | C | 49.5% | inf / inf | 210 | coding (133/366 nt) | fliO | flagellar biosynthesis protein FliO |
| * | NC_000913 | 1,248,829 | 0 | A | G | 49.2% | 30.2 / inf | 244 | C96R (TGT→CGT) | dhaM | dihydroxyacetone kinase subunit M |
| * | NC_000913 | 357,793 | 0 | A | G | 48.3% | 77.4 / inf | 346 | *300Q (TAG→CAG) | cynR | DNA‑binding transcriptional dual regulator CynR |
| * | NC_000913 | 2,504,444 | 0 | T | C | 46.7% | 94.0 / inf | 306 | L14L (CTA→CTG) | fryA | putative PTS multiphosphoryl transfer protein FryA |
| * | NC_000913 | 3,129,751 | 0 | G | A | 42.4% | 156.4 / inf | 271 | D155D (GAC→GAT) | yghO | putative DNA‑binding transcriptional regulator YghO |
| * | NC_000913 | 402,965 | 0 | G | T | 41.4% | 372.9 / inf | 275 | G407C (GGC→TGC) | phoA | alkaline phosphatase |
| * | NC_000913 | 2,462,880 | 1 | . | C | 39.4% | 43.9 / 146.3 | 72 | intergenic (+234/‑132) | fadL/yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| * | NC_000913 | 1,001,016 | 0 | A | . | 38.6% | 777.0 / inf | 282 | coding (1801/2601 nt) | elfC | putative fimbrial usher protein ElfC |
| * | NC_000913 | 995,636 | 0 | C | T | 37.6% | 339.6 / inf | 340 | G118D (GGC→GAC) | ssuD | FMNH2‑dependent alkanesulfonate monooxygenase |
| * | NC_000913 | 4,606,322 | 1 | . | G | 35.9% | 260.5 / inf | 220 | noncoding (80/87 nt) | leuQ | tRNA‑Leu |
| * | NC_000913 | 4,606,087 | 0 | G | . | 34.1% | 592.9 / inf | 217 | noncoding (79/87 nt) | leuV | tRNA‑Leu |
| * | NC_000913 | 2,536,819 | 0 | T | C | 30.1% | 539.8 / inf | 326 | D140G (GAC→GGC) | pdxK | pyridoxal kinase I |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.2% | 1086.3 / inf | 553 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 604,407 | 0 | A | G | 25.8% | 579.2 / 241.2 | 292 | V86A (GTA→GCA) | ybdG | miniconductance mechanosensitive channel YbdG |
| * | NC_000913 | 495,028 | 0 | C | T | 24.6% | 541.0 / 212.8 | 268 | intergenic (+18/‑92) | recR/htpG | DNA repair protein RecR/chaperone protein HtpG |
| * | NC_000913 | 3,924,265 | 0 | G | A | 20.8% | 597.6 / 168.6 | 250 | L457L (CTG→TTG) | mnmG | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| * | NC_000913 | 3,076,176 | 0 | A | G | 20.2% | 795.7 / 186.8 | 312 | S3P (TCC→CCC) | yggF | fructose 1,6‑bisphosphatase YggF |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 260 (0.860) | 69 (0.270) | 56/164 | 11.5 | 25.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 186 (0.740) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1207790 = | 247 (0.820) | 61 (0.240) | 53/164 | 12.4 | 23.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 192 (0.760) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 71350 | 328 (1.080) | 110 (0.370) | 53/190 | 15.5 | 40.9% | intergenic (+85/‑1) | araC/yabI | DNA‑binding transcriptional dual regulator AraC/DedA family protein YabI |
| ? | NC_000913 | = 2857042 | 0 (0.000) | intergenic (‑236/‑51) | ygbA/mutS | protein YgbA/DNA mismatch repair protein MutS | |||||
| * | ? | NC_000913 | = 1209618 | 245 (0.810) | 10 (0.040) | 9/166 | 33.9 | 4.0% | pseudogene (38/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment |
| ? | NC_000913 | 2471897 = | 271 (1.060) | pseudogene (166/519 nt) | yfdL | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL | |||||
| * | ? | NC_000913 | = 4542690 | 394 (1.300) | 7 (0.030) | 7/178 | 37.0 | 1.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 356 (1.300) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 393 (1.300) | 5 (0.020) | 5/178 | 38.9 | 1.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 357 (1.300) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1771236 = | 280 (0.920) | 91 (0.300) | 3/196 | 43.0 | 24.5% | coding (166/1215 nt) | ydiM | putative exporter YdiM |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||