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 | 34.1% | G212G (GGC→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 36,576 | C→T | 8.3% | V417I (GTC→ATC) | caiC ← | carnitine‑CoA ligase |
| RA | 123,466 | T→G | 25.0% | A150A (GCT→GCG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 125,336 | C→T | 6.2% | R774C (CGC→TGC) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 167,786 | A→C | 25.1% | E101D (GAA→GAC) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 343,070 | G→C | 7.7% | E63Q (GAA→CAA) | yahK → | aldehyde reductase, NADPH‑dependent |
| RA | 357,103 | T→C | 6.0% | F311F (TTT→TTC) | codA → | cytosine/isoguanine deaminase |
| RA | 497,594 | G→C | 36.4% | P140P (CCG→CCC) | adk → | adenylate kinase |
| RA | 497,610 | G→C | 37.5% | D146H (GAC→CAC) | adk → | adenylate kinase |
| RA | 531,187 | G→T | 9.3% | L14M (CTG→ATG) | selU ← | tRNA 2‑selenouridine synthase |
| RA | 652,898 | C→G | 13.8% | R222G (CGT→GGT) | dpiB → | sensory histidine kinase DpiB |
| RA | 676,168 | G→A | 6.1% | A127V (GCG→GTG) | ybeQ ← | Sel1 repeat‑containing protein YbeQ |
| RA | 729,372 | A→C | 40.1% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 739,484 | A→T | 5.4% | N162Y (AAC→TAC) | ybgA → | DUF1722 domain‑containing protein YbgA |
| RA | 896,791 | G→T | 9.3% | D220Y (GAT→TAT) | potH → | putrescine ABC transporter membrane subunit PotH |
| RA | 935,439 | T→C | 9.3% | V739A (GTA→GCA) | ftsK → | cell division DNA translocase FtsK |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,434,996 | G→T | 11.9% | pseudogene (13/51 nt) | ttcC ← | putative tRNA 2‑thiocytidine (s(2)C32) synthase |
| RA | 1,435,939 | C→T | 5.1% | V319I (GTT→ATT) | ompN ← | outer membrane porin N |
| RA | 1,459,597 | C→A | 10.5% | R182S (CGC→AGC) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase |
| RA | 1,478,602 | G→T | 6.8% | G126V (GGT→GTT) | ynbB → | putative CDP‑diglyceride synthase |
| RA | 1,657,338 | A→G | 5.1% | D40D (GAT→GAC) | ynfC ← | UPF0257 family lipoprotein YnfC |
| RA | 1,690,317 | G→T | 8.6% | D156Y (GAT→TAT) | ydgA → | conserved protein YdgA |
| RA | 1,856,087 | C→T | 10.6% | R281H (CGC→CAC) | ydjH ← | putative sugar kinase YdjH |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,054,412 | C→T | 6.0% | A257V (GCG→GTG) | shiA → | shikimate:H(+) symporter |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,234 | C→A | 52.7% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 56.5% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,189,612 | C→A | 8.1% | S433S (TCG→TCT) | yehB ← | putative fimbrial usher protein YehB |
| RA | 2,407,626 | G→A | 7.0% | L22L (CTG→CTA) | alaA → | glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,412,061 | A→G | 6.7% | L10P (CTT→CCT) | hxpA ← | hexitol phosphatase A |
| RA | 2,496,198 | Δ1 bp | 6.2% | coding (554/921 nt) | lpxP → | palmitoleoyl acyltransferase |
| RA | 2,496,199 | Δ1 bp | 6.2% | coding (555/921 nt) | lpxP → | palmitoleoyl acyltransferase |
| RA | 2,582,860 | C→T | 5.5% | intergenic (‑83/+43) | ypfG ← / ← nudK | DUF1176 domain‑containing protein YpfG/GDP‑mannose hydrolase |
| RA | 2,592,130 | A→G | 6.6% | N175S (AAT→AGT) | dapE → | succinyl‑diaminopimelate desuccinylase |
| RA | 2,696,334 | G→C | 5.8% | K178N (AAG→AAC) | mltF → | membrane‑bound lytic murein transglycosylase F |
| RA | 2,765,525 | T→C | 6.2% | P84P (CCA→CCG) | yfjM ← | CP4‑57 prophage; protein YfjM |
| RA | 2,848,129 | G→A | 6.0% | A371A (GCC→GCT) | hycC ← | formate hydrogenlyase subunit HycC |
| RA | 3,016,756 | C→T | 7.5% | P233S (CCG→TCG) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,272,687 | G→C | 6.8% | A22G (GCA→GGA) | garR ← | tartronate semialdehyde reductase |
| RA | 3,322,187 | C→T | 6.0% | D107N (GAT→AAT) | secG ← | Sec translocon subunit SecG |
| RA | 3,353,707 | A→T | 5.9% | V115E (GTG→GAG) | yhcC ← | radical SAM family oxidoreductase YhcC |
| MC JC | 3,384,721 | Δ435 bp | 100% | coding (19‑453/471 nt) | argR → | DNA‑binding transcriptional dual regulator ArgR |
| RA | 3,454,069 | G→T | 26.7% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,523,181 | C→T | 6.8% | A104V (GCA→GTA) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| JC | 3,816,605 | Δ103 bp | 14.2% | [yicC] | [yicC] | |
| RA | 3,828,985 | T→G | 45.0% | V14G (GTT→GGT) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,877,635 | C→A | 38.9% | intergenic (‑170/+70) | yidB ← / ← gyrB | conserved protein YidB/DNA gyrase subunit B |
| RA | 4,096,637 | A→T | 8.9% | F271Y (TTT→TAT) | rhaB ← | rhamnulokinase |
| RA | 4,182,820 | C→T | 76.3% | H526Y (CAC→TAC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,188,573 | G→T | 9.2% | R1075L (CGT→CTT) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,190,539 | G→A | 7.3% | intergenic (‑52/+196) | sroH ← / ← thiH | small RNA SroH/2‑iminoacetate synthase |
| RA | 4,230,291 | C→T | 7.3% | intergenic (‑149/‑63) | pepE ← / → rluF | peptidase E/23S rRNA pseudouridine(2604) and tRNA(Tyr) pseudouridine(35) synthase |
| RA | 4,283,228 | T→G | 50.6% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 30.0% | 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 | 4,405,366 | C→T | 5.9% | T227M (ACG→ATG) | purA → | adenylosuccinate synthetase |
| RA | 4,478,951 | A→T | 8.5% | intergenic (+62/+83) | rraB → / ← yjgM | ribonuclease E inhibitor protein B/putative acetyltransferase YjgM |
| RA | 4,556,759 | G→T | 5.5% | G36C (GGT→TGT) | ytiD → | protein YtiD |
| RA | 4,610,345 | A→C | 20.4% | H311P (CAC→CCC) | prfC → | peptide chain release factor RF3 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423769–3424234 | 3424532–3424238 | 5–764 | 15 [12] | [13] 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 = | 33 (0.650) | 27 (0.620) | 19/202 | NT | 57.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 12 (0.270) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 35 (0.690) | 20 (0.460) | 17/202 | NT | 48.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 12 (0.270) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 3815877 | 36 (0.710) | 4 (0.080) | 4/232 | NT | 9.3% | coding (673/687 nt) | rph | truncated RNase PH |
| ? | NC_000913 | 3816138 = | 42 (0.840) | coding (412/687 nt) | rph | truncated RNase PH | |||||