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 | 18,124 | C→G | 29.5% | G212G (GGC→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 79,011 | A→G | 5.9% | L148P (CTG→CCG) | leuD ← | 3‑isopropylmalate dehydratase subunit LeuD |
| RA | 231,794 | T→G | 20.8% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase domain‑containing protein YafD |
| RA | 238,497 | G→T | 20.1% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 262,033 | T→A | 5.5% | D177E (GAT→GAA) | proA → | glutamate‑5‑semialdehyde dehydrogenase |
| RA | 375,488 | A→G | 6.9% | S10S (TCA→TCG) | mhpT → | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 426,761 | G→A | 5.5% | G209S (GGC→AGC) | tgt → | tRNA‑guanine transglycosylase |
| RA | 454,877 | A→T | 45.0% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 497,585 | C→A | 26.4% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | 548,153 | T→G | 24.7% | L492V (TTA→GTA) | fdrA → | putative acyl‑CoA synthetase FdrA |
| RA | 571,498 | G→A | 5.6% | R15R (CGG→CGA) | ybcM → | DLP12 prophage; putative DNA‑binding transcriptional regulator |
| RA | 623,491 | C→G | 16.4% | L398V (CTG→GTG) | entS → | enterobactin exporter EntS |
| RA | 630,842 | A→G | 7.9% | T317A (ACT→GCT) | cstA → | carbon starvation protein A |
| RA | 729,383 | T→G | 44.6% | intergenic (+43/‑200) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 820,638 | C→A | 23.5% | intergenic (+50/‑155) | ybhL → / → ybhM | Bax1‑I family protein YbhL/Bax1‑I family protein YbhM |
| RA | 825,317 | A→G | 7.4% | G264G (GGT→GGC) | ybhR ← | putative ABC exporter membrane subunit YbhR |
| RA | 906,799 | A→T | 6.3% | intergenic (‑46/+53) | ybjS ← / ← ybjT | putative NAD(P)H‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/putative NAD(P)‑dependent oxidoreductase YbjT |
| RA | 972,305 | T→A | 5.5% | L185* (TTA→TAA) | ycbJ → | putative phosphotransferase YcbJ |
| RA | 1,010,570 | A→G | 8.5% | N203D (AAC→GAC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,254,034 | T→G | 19.0% | N640T (AAC→ACC) | ycgV ← | putative autotransporter adhesin YcgV |
| RA | 1,265,246 | C→T | 6.4% | Q79* (CAG→TAG) | prfA → | peptide chain release factor RF1 |
| JC JC | 1,293,037 | IS1 (–) +9 bp | 34.3% | intergenic (‑115/‑482) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| JC JC | 1,424,666 | IS5 (+) +4 bp | 16.1% | coding (885‑888/1458 nt) | trkG → | Rac prophage; K(+) transporter TrkG |
| RA | 1,429,943 | A→T | 11.3% | K299* (AAA→TAA) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,480,706 | G→C | 6.4% | W523C (TGG→TGC) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,480,737 | T→C | 6.6% | L534L (TTA→CTA) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,508,762 | C→T | 6.9% | intergenic (+20/+72) | rlhA → / ← yncJ | 23S rRNA 5‑hydroxycytidine C2501 synthase/protein YncJ |
| RA | 1,519,943 | A→T | 6.6% | D306V (GAT→GTT) | curA → | NADPH‑dependent curcumin/dihydrocurcumin reductase |
| RA | 1,622,357 | C→A | 9.5% | G342G (GGC→GGA) | ydeE → | dipeptide exporter |
| RA | 1,643,012 | T→C | 5.3% | N77S (AAC→AGC) | ydfT ← | Qin prophage; putative antitermination protein Q |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,982,269 | T→C | 7.1% | N40S (AAT→AGT) | otsB ← | trehalose‑6‑phosphate phosphatase |
| RA | 2,039,759 | G→T | 8.1% | G94G (GGG→GGT) | msrP → | periplasmic protein‑L‑methionine sulfoxide reductase catalytic subunit |
| RA | 2,126,020 | G→A | 5.7% | A68V (GCG→GTG) | gmm ← | GDP‑mannose mannosyl hydrolase |
| RA | 2,139,598 | T→G | 35.6% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,245 | G→T | 64.5% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,265 | A→T | 14.4% | intergenic (‑61/+247) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,248,918 | A→T | 7.8% | I234N (ATT→AAT) | yeiE ← | putative LysR‑type transcriptional regulator YeiE |
| RA | 2,292,439 | A→T | 7.7% | W176R (TGG→AGG) | ccmG ← | holocytochrome c synthetase ‑ thiol:disulfide oxidoreductase CcmG |
| RA | 2,314,181 | G→T | 22.9% | D232Y (GAT→TAT) | rcsD → | RcsD phosphotransferase |
| RA | 2,715,558 | A→G | 6.8% | M46V (ATG→GTG) | eamB → | cysteine/O‑acetylserine exporter EamB |
| RA | 2,870,535 | G→T | 10.1% | A257D (GCC→GAC) | truD ← | tRNA pseudouridine(13) synthase |
| RA | 2,872,863 | G→C | 16.3% | intergenic (‑43/+151) | ftsB ← / ← ygbE | cell division protein FtsB/conserved inner membrane protein YgbE |
| RA | 3,233,311 | G→A | 5.8% | M549I (ATG→ATA) | fadH → | 2,4‑dienoyl‑CoA reductase |
| RA | 3,253,114 | C→A | 8.7% | I68I (ATC→ATA) | yhaI → | putative inner membrane protein |
| RA | 3,448,218 | A→C | 26.0% | intergenic (‑69/+96) | rplN ← / ← rpsQ | 50S ribosomal subunit protein L14/30S ribosomal subunit protein S17 |
| RA | 3,454,069 | G→T | 22.0% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,468,124 | A→C | 17.9% | V577G (GTA→GGA) | chiA ← | endochitinase |
| RA | 3,539,011 | G→T | 5.4% | G543W (GGG→TGG) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,558,205 | G→T | 7.3% | intergenic (‑126/‑63) | rtcB ← / → rtcR | RNA‑splicing ligase/DNA‑binding transcriptional activator RtcR |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,593,690 | Δ1 bp | 6.2% | coding (517/768 nt) | livG ← | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivG |
| RA | 3,593,691 | Δ1 bp | 6.2% | coding (516/768 nt) | livG ← | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivG |
| RA | 3,812,126 | A→T | 10.4% | L145Q (CTA→CAA) | yicR ← | RadC‑like JAB domain‑containing protein YicR |
| RA | 3,828,980 | A→C | 36.6% | Q12H (CAA→CAC) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,828,985 | T→G | 36.3% | V14G (GTT→GGT) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,968,665 | Δ1 bp | 6.7% | coding (750/1104 nt) | rfe → | UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase |
| RA | 4,005,854 | C→T | 9.1% | intergenic (+123/‑10) | pldA → / → recQ | outer membrane phospholipase A/ATP‑dependent DNA helicase RecQ |
| RA | 4,028,255 | T→G | 26.1% | H173P (CAC→CCC) | fadA ← | 3‑ketoacyl‑CoA thiolase |
| MC JC | 4,123,449 | Δ990 bp | 100% | coding (19‑1008/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,185,642 | G→A | 59.3% | R98H (CGC→CAC) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,228,313 | A→C | 17.0% | T195P (ACC→CCC) | yjbB → | putative inorganic phosphate export protein |
| RA | 4,296,060 | C→T | 30.8% | 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 | 4,447,271 | A→G | 6.2% | N1054D (AAT→GAT) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,491,374 | A→C | 12.6% | G384G (GGT→GGG) | idnT ← | L‑idonate/5‑ketogluconate/gluconate transporter |
| RA | 4,532,747 | A→G | 6.2% | L146P (CTA→CCA) | yjhP ← | KpLE2 phage‑like element; putative methyltransferase YjhP |
| RA | 4,572,008 | A→T | 6.0% | intergenic (+93/‑406) | yjiS → / → yjiT | DUF1127 domain‑containing protein YjiS/putative uncharacterized protein YjiT |
| RA | 4,639,719 | C→G | 19.3% | P196P (CCG→CCC) | arcA ← | DNA‑binding transcriptional dual regulator ArcA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 164549 | 164624 | 76 | 20 [14] | [15] 17 | hrpB/mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | * | ÷ | NC_000913 | 3423769–3424234 | 3424539–3424238 | 5–771 | 24 [16] | [14] 17 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 22 (0.370) | 37 (0.720) | 29/204 | NT | 62.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 26 (0.510) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 22 (0.370) | 25 (0.490) | 21/204 | NT | 52.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 26 (0.510) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 69 (1.200) | 42/228 | NT | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 35 (0.590) | 31/236 | NT | 40.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3837175 | 52 (0.880) | coding (223/1185 nt) | setC | putative arabinose exporter | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 54 (0.910) | 37/236 | NT | 45.8% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3704772 = | 64 (1.080) | coding (1019/1020 nt) | dppB | dipeptide ABC transporter membrane subunit DppB | |||||