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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 665,856 | A→G | 44.7% | L153P (CTG→CCG) | mrdB ← | cell wall shape‑determining protein |
| RA | 758,697 | G→T | 49.9% | intergenic (+292/‑9) | sdhB → / → sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| JC | 762,329 | Δ19 bp | 17.2% | coding (808‑826/1218 nt) | sucB → | dihydrolipoyltranssuccinase |
| RA | 1,286,866 | A→G | 10.3% | intergenic (+340/+200) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,286,870 | C→A | 7.8% | intergenic (+344/+196) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,286,874 | G→A | 8.5% | intergenic (+348/+192) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,466,438 | T→G | 8.1% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,081,912 | G→T | 6.6% | I212I (ATC→ATA) | dacD ← | D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,478,545 | C→T | 5.1% | F233F (TTC→TTT) | dsdX → | D‑serine transporter |
| RA | 2,778,903 | Δ1 bp | 6.1% | coding (3824/4581 nt) | ypjA ← | adhesin‑like autotransporter |
| JC JC | 2,876,678 | IS5 (+) +4 bp | 35.9% | coding (98‑101/1038 nt) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 3,372,184 | T→A | 11.4% | T131S (ACC→TCC) | nanT ← | sialic acid transporter |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,950,469 | T→G | 5.2% | intergenic (+49/‑38) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 7.0% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 18.4% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 20.5% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 20.9% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 13.7% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 6.8% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583080 | 584689 | 1610 | 33 [32] | [31] 34 | [tfaX]–[ompT] | [tfaX],appY,[ompT] |
| * | * | ÷ | NC_000913 | 755127 | 758427 | 3301 | 33 [32] | [32] 33 | sdhC–sdhB | sdhC,sdhD,sdhA,sdhB |
| * | * | ÷ | NC_000913 | 2469046 | 2470752 | 1707 | 33 [32] | [31] 34 | [gtrB]–gtrS | [gtrB],gtrS |
| * | * | ÷ | NC_000913 | 2988726 | 2991674 | 2949 | 33 [32] | [32] 33 | [yqeI]–[ygeG] | [yqeI],yqeJ,yqeL,yqeK,ygeF,ygeF,[ygeG] |
| * | * | ÷ | NC_000913 | 3423873–3424232 | 3424401–3424238 | 7–529 | 33 [31] | [31] 34 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3796808 | 3800535 | 3728 | 34 [32] | [32] 33 | [waaC]–[waaY] | [waaC],waaL,waaU,waaZ,[waaY] |
| * | * | ÷ | NC_000913 | 3804062 | 3805293 | 1232 | 33 [32] | [32] 33 | [waaB]–[waaP] | [waaB],waaS,[waaP] |
| * | * | ÷ | NC_000913 | 4541474 | 4541981 | 508 | 35 [31] | [32] 34 | [fimB] | [fimB] |
| * | * | ÷ | NC_000913 | 4542500 | 4542990 | 491 | 33 [31] | [31] 35 | [fimE] | [fimE] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315413 | 36 (0.380) | 3 (0.030) | 3/486 | NT | 8.1% | noncoding (185/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315613 | NA (NA) | noncoding (385/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 689045 | NA (NA) | 4 (0.040) | 4/510 | NT | 8.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 754750 | 41 (0.430) | intergenic (‑282/‑427) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 | |||||
| * | ? | NC_000913 | 1207790 = | 50 (0.520) | 40 (0.450) | 36/480 | NT | 51.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 30 (0.330) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 50 (0.520) | 34 (0.380) | 27/480 | NT | 46.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 30 (0.330) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 4544926 = | 69 (0.720) | 4 (0.040) | 4/498 | NT | 5.6% | coding (623/726 nt) | fimC | periplasmic chaperone |
| ? | NC_000913 | 4545203 = | 69 (0.740) | coding (108/2637 nt) | fimD | fimbrial usher outer membrane porin protein; FimCD chaperone‑usher | |||||