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 | 125,085 | T→A | 100% | I690N (ATC→AAC) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 272,330:1 | +G | 15.4% | intergenic (+140/‑250) | insN → / → eyeA | CP4‑6 prophage; IS911A regulator fragment/CP4‑6 prophage; small RNA EyeA |
| RA | 463,457 | G→A | 45.0% | G515S (GGT→AGT) | ppiD → | periplasmic folding chaperone |
| JC JC | 568,268 | IS1 (–) +9 bp | 100% | intergenic (+21/‑39) | renD → / → emrE | DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE |
| RA | 699,559 | A→G | 26.1% | intergenic (‑382/+15) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 100% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 100% | L375L (TTA→CTA) | icd → | isocitrate dehydrogenase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,570,512 | C→T | 100% | intergenic (‑23/+133) | gadC ← / ← gadB | L‑glutamate:4‑aminobutyrate antiporter/glutamate decarboxylase B |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,323,330 | C→T | 29.5% | intergenic (+79/‑117) | atoC → / → atoD | DNA‑binding transcriptional activator/ornithine decarboxylase inhibitor AtoC/acetyl‑CoA:acetoacetyl‑CoA transferase subunit alpha |
| RA | 2,534,156 | A→T | 40.0% | I31F (ATT→TTT) | ptsI → | PTS enzyme I |
| RA | 2,661,816 | T→G | 71.0% | T106P (ACC→CCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,351,007 | Δ1 bp | 35.3% | coding (2019/2337 nt) | arcB ← | sensory histidine kinase ArcB |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,137,914 | C→T | 8.3% | intergenic (‑257/+18) | yijF ← / ← gldA | conserved protein YijF/L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 30.5% | 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 | 4,324,917 | T→C | 13.2% | K83K (AAA→AAG) | phnC ← | phosphonate ABC transporter ATP binding subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196297 | 1211435 | 15139 | 4 [3] | [3] 4 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 2066293–2066464 | 2066611–2066466 | 3–319 | 4 [3] | [3] 4 | [insH‑6] | [insH‑6] |
| * | * | ÷ | NC_000913 | 3423754–3424234 | 3424514–3424240 | 7–761 | 4 [3] | [3] 4 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3621199–3622296 | 3653127–3652031 | 29736–31929 | 4 [3] | [2] 4 | [rhsB]–[insH‑11] | [rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 285319 = | 10 (0.480) | 3 (0.160) | 3/244 | NT | 18.6% | intergenic (+151/‑76) | yagF/yagG | CP4‑6 prophage; D‑xylonate dehydratase/putative D‑xylonate transporter YagG |
| ? | NC_000913 | 285411 = | 17 (0.890) | coding (17/1383 nt) | yagG | putative D‑xylonate transporter YagG | |||||
| * | ? | NC_000913 | = 609351 | NA (NA) | 6 (0.300) | 6/256 | NT | 35.3% | noncoding (1345/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 2227427 = | 11 (0.550) | pseudogene (1332/1436 nt) | mdtQ | putative multidrug resistance outer membrane protein MdtQ | |||||
| * | ? | NC_000913 | = 2067353 | NA (NA) | 5 (0.250) | 4/258 | NT | 29.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2079471 = | 12 (0.580) | intergenic (‑110/+62) | yeeX/yeeA | DUF496 domain‑containing protein YeeX/putative transporter YeeA | |||||
| * | ? | NC_000913 | = 3352023 | 4 (0.190) | 6 (0.290) | 6/262 | NT | 60.0% | coding (1003/2337 nt) | arcB | sensory histidine kinase ArcB |
| ? | NC_000913 | 3365556 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 4012917 = | 30 (1.450) | 4 (0.200) | 4/256 | NT | 12.3% | intergenic (‑101/‑136) | metR/metE | DNA‑binding transcriptional dual regulator MetR/cobalamin‑independent homocysteine transmethylase |
| ? | NC_000913 | 4013018 = | 28 (1.400) | intergenic (‑202/‑35) | metR/metE | DNA‑binding transcriptional dual regulator MetR/cobalamin‑independent homocysteine transmethylase | |||||
| * | ? | NC_000913 | 4306577 = | 30 (1.450) | 3 (0.150) | 3/250 | NT | 9.9% | coding (21/1986 nt) | yjcS | alkyl sulfatase |
| ? | NC_000913 | 4306596 = | 26 (1.330) | coding (2/1986 nt) | yjcS | alkyl sulfatase | |||||