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 |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 40,687 | G→A | 7.2% | C415C (TGC→TGT) | caiT ← | L‑carnitine:gamma‑butyrobetaine antiporter |
| RA | 94,270 | T→A | 6.9% | L369I (TTA→ATA) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 219,874 | G→A | 7.2% | P41L (CCG→CTG) | rcsF ← | outer membrane lipoprotein RcsF |
| RA | 238,523 | G→T | 25.7% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 29.8% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 273,571 | G→A | 7.7% | R242H (CGC→CAC) | ykfC → | CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 284,059 | A→C | 20.8% | T287P (ACG→CCG) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 454,873 | C→G | 49.6% | intergenic (+84/‑260) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 497,291 | C→A | 9.1% | V39V (GTC→GTA) | adk → | adenylate kinase |
| RA | 504,684 | C→T | 8.2% | E5K (GAA→AAA) | fsr ← | fosmidomycin efflux pump |
| RA | 508,238 | A→C | 20.9% | K7N (AAA→AAC) | ybaQ → | putative DNA‑binding transcriptional regulator YbaQ |
| RA | 705,533 | G→A | 9.1% | A530A (GCG→GCA) | nagE → | N‑acetylglucosamine specific PTS enzyme IIABC component |
| RA | 738,130 | C→A | 5.3% | I13I (ATC→ATA) | ybfD → | H repeat‑associated putative transposase YbfD |
| RA | 778,296 | A→T | 7.3% | D186V (GAC→GTC) | tolB → | Tol‑Pal system periplasmic protein TolB |
| RA | 835,254 | T→A | 7.3% | Y3N (TAT→AAT) | ybiB → | nonspecific DNA‑binding protein YbiB |
| MC JC | 932,613 | Δ459 bp | 100% | coding (19‑477/495 nt) | lrp → | DNA‑binding transcriptional dual regulator Lrp |
| RA | 962,819 | G→A | 8.0% | P275P (CCG→CCA) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 999,766 | C→G | 7.9% | A184G (GCT→GGT) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,248,994 | G→A | 7.7% | P41S (CCA→TCA) | dhaM ← | dihydroxyacetone kinase subunit M |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,333,643 | T→C | 65.4% | *866Q (TAA→CAA) | topA → | DNA topoisomerase 1 |
| RA | 1,425,597 | T→G | 21.8% | V74G (GTC→GGC) | ynaK → | Rac prophage; ParB‑like nuclease domain‑containing protein YnaK |
| RA | 1,599,032 | A→T | 11.1% | L393* (TTG→TAG) | lsrK ← | autoinducer‑2 kinase |
| RA | 1,615,131 | G→A | 6.2% | E110K (GAA→AAA) | yneJ → | putative LysR‑type DNA‑binding transcriptional regulator YneJ |
| RA | 1,738,698 | G→A | 7.7% | P285P (CCG→CCA) | purR → | DNA‑binding transcriptional repressor PurR |
| RA | 1,755,972 | Δ1 bp | 65.7% | coding (275/1413 nt) | pykF → | pyruvate kinase I |
| RA | 1,886,895 | A→G | 13.3% | L366S (TTA→TCA) | rnd ← | RNase D |
| RA | 1,956,070 | T→C | 9.1% | K313R (AAG→AGG) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,983,854 | G→T | 7.4% | Q406K (CAA→AAA) | araG ← | arabinose ABC transporter ATP binding subunit |
| RA | 2,043,194 | G→T | 25.5% | intergenic (+296/+274) | yodB → / ← serU | putative cytochrome/tRNA‑Ser |
| RA | 2,070,520 | T→C | 5.9% | intergenic (+46/‑266) | yoeA → / → yeeP | CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA/CP4‑44 prophage; putative GTP‑binding protein |
| RA | 2,139,598 | T→G | 31.6% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,166,222 | G→C | 17.7% | K185N (AAG→AAC) | yegQ → | putative peptidase YegQ |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,313,835 | T→C | 7.3% | S116S (TCT→TCC) | rcsD → | RcsD phosphotransferase |
| RA | 2,666,405 | T→G | 17.7% | V324G (GTG→GGG) | csiE → | stationary phase inducible protein CsiE |
| RA | 2,734,761 | Δ1 bp | 76.9% | coding (274/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,734,762 | Δ1 bp | 76.9% | coding (273/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,868,312 | G→A | 5.1% | R148C (CGC→TGC) | nlpD ← | murein hydrolase activator NlpD |
| RA | 2,901,776 | G→A | 8.3% | M395I (ATG→ATA) | yqcE → | putative transport protein YqcE |
| RA | 3,036,145 | A→G | 11.1% | V46A (GTC→GCC) | prfB ← | peptide chain release factor RF2 |
| RA | 3,199,111 | A→G | 6.2% | I177I (ATT→ATC) | glnE ← | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
| RA | 3,224,782 | T→C | 6.3% | L717P (CTG→CCG) | ebgA → | evolved beta‑D‑galactosidase subunit alpha |
| RA | 3,247,150 | T→C | 10.0% | W167R (TGG→CGG) | exuR → | DNA‑binding transcriptional repressor ExuR |
| RA | 3,247,615 | T→G | 5.4% | intergenic (+187/‑158) | exuR → / → yqjA | DNA‑binding transcriptional repressor ExuR/DedA family protein YqjA |
| RA | 3,304,688 | G→A | 5.2% | P377L (CCG→CTG) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,377,240 | T→G | 15.6% | T61P (ACC→CCC) | sspA ← | stringent starvation protein A |
| RA | 3,377,430 | C→T | 72.3% | intergenic (‑10/+385) | sspA ← / ← rpsI | stringent starvation protein A/30S ribosomal subunit protein S9 |
| RA | 3,422,132 | T→G | 27.2% | L270V (TTG→GTG) | yhdY → | putative ABC transporter membrane subunit YhdY |
| RA | 3,452,945 | G→A | 6.8% | intergenic (‑19/+14) | rplC ← / ← rpsJ | 50S ribosomal subunit protein L3/30S ribosomal subunit protein S10 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,597,134 | G→A | 6.2% | L143L (CTG→TTG) | livK ← | L‑leucine/L‑phenylalanine ABC transporter periplasmic binding protein |
| RA | 3,755,059 | C→T | 7.2% | E485K (GAA→AAA) | aldB ← | aldehyde dehydrogenase B |
| RA | 3,829,990 | Δ1 bp | 6.6% | coding (1046/1392 nt) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,866,701 | G→A | 10.0% | T66M (ACG→ATG) | ibpB ← | small heat shock protein IbpB |
| RA | 3,996,063 | C→T | 9.1% | H161Y (CAC→TAC) | yigA → | conserved protein YigA |
| RA | 4,028,244 | A→C | 33.9% | W177G (TGG→GGG) | fadA ← | 3‑ketoacyl‑CoA thiolase |
| RA | 4,059,540 | C→T | 7.2% | F378F (TTC→TTT) | bipA → | ribosome‑dependent GTPase, ribosome assembly factor |
| RA | 4,081,148 | G→A | 7.7% | F27F (TTC→TTT) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,147,699 | G→T | 31.2% | Q207K (CAA→AAA) | yijO ← | putative DNA‑binding transcriptional regulator YijO |
| RA | 4,296,060 | C→T | 16.5% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,430,091 | A→G | 11.4% | E76E (GAA→GAG) | cycA → | serine/alanine/glycine/cycloserine:H(+)symporter |
| RA | 4,478,808 | C→A | 58.4% | G112G (GGC→GGA) | rraB → | ribonuclease E inhibitor protein B |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 164551 | 164622 | 72 | 15 [12] | [12] 13 | hrpB/mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | * | ÷ | NC_000913 | 915183–915194 | 915246 | 53–64 | 14 [11] | [12] 15 | lysO/aqpZ | L‑lysine exporter/water channel AqpZ |
| * | * | ÷ | NC_000913 | 3423750–3424524 | 3424524 | 1–775 | 14 [11] | [11] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 29 (0.620) | 20 (0.490) | 14/204 | NT | 52.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 11 (0.270) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 29 (0.620) | 17 (0.420) | 16/204 | NT | 48.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 11 (0.270) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1755755 = | 54 (1.160) | 4 (0.090) | 3/236 | NT | 6.9% | coding (58/1413 nt) | pykF | pyruvate kinase I |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 4498180 = | NA (NA) | 4 (0.090) | 4/236 | NT | NA | intergenic (+240/‑92) | intB/insC‑6 | KpLE2 phage‑like element; putative integrase/KpLE2 phage‑like element; IS2 insertion element repressor InsA |
| ? | NC_000913 | = 4499511 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||