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 | annotation | gene | description |
| RA | 43,425 | G→T | A80S (GCA→TCA) | fixB → | putative electron transfer flavoprotein FixB |
| RA | 114,053 | G→T | E204* (GAA→TAA) | guaC → | GMP reductase |
| RA | 139,245 | C→A | G661C (GGT→TGT) | gcd ← | quinoprotein glucose dehydrogenase |
| RA | 229,081 | C→A | intergenic (+77/‑86) | aspU → / → dkgB | tRNA‑Asp/methylglyoxal reductase DkgB |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 289,414 | C→A | G298W (GGG→TGG) | argF ← | CP4‑6 prophage; ornithine carbamoyltransferase ArgF |
| RA | 330,549 | C→A | L363M (CTG→ATG) | betT → | choline:H(+) symporter |
| RA | 388,636 | G→T | R281L (CGG→CTG) | tauD → | taurine dioxygenase |
| RA | 391,777 | G→T | L277I (CTC→ATC) | insF‑2 ← | IS3 element protein InsF |
| RA | 437,372 | Δ1 bp | coding (764/975 nt) | yajO ← | 1‑deoxyxylulose‑5‑phosphate synthase YajO |
| RA | 457,774 | C→A | L117M (CTG→ATG) | clpX → | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | 487,967 | G→T | A478S (GCG→TCG) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 641,517 | C→A | S117S (TCG→TCT) | uspG ← | universal stress protein G |
| RA | 681,397 | C→A | P396T (CCG→ACG) | djlC → | co‑chaperone DjlC |
| RA | 744,706 | C→T | S155L (TCG→TTG) | pxpC → | 5‑oxoprolinase component C |
| RA | 756,216 | C→A | L104M (CTG→ATG) | sdhA → | succinate:quinone oxidoreductase, FAD binding protein |
| RA | 779,696 | C→A | V33V (GTC→GTA) | cpoB → | cell division coordinator CpoB |
| RA | 790,725 | G→T | A102E (GCG→GAG) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 796,078 | C→A | R73S (CGC→AGC) | modB → | molybdate ABC transporter membrane subunit |
| RA | 800,423 | C→A | E51D (GAG→GAT) | ybhD ← | putative DNA‑binding transcriptional regulator YbhD |
| RA | 828,800 | C→A | S61I (AGC→ATC) | ybhF ← | putative ABC exporter ATP binding subunit |
| RA | 879,567 | G→T | G276W (GGG→TGG) | yliI → | aldose sugar dehydrogenase YliI |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 906,254 | C→A | R167L (CGC→CTC) | ybjS ← | putative NAD(P)H‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 980,755 | G→T | G1477V (GGA→GTA) | mukB → | chromosome partitioning protein MukB |
| RA | 1,019,359 | G→T | P232Q (CCG→CAG) | ompA ← | outer membrane porin A |
| RA | 1,113,836 | C→A | A116S (GCA→TCA) | msyB ← | acidic protein that suppresses heat sensitivity of a secY mutant |
| RA | 1,154,311 | G→T | R67L (CGG→CTG) | mltG → | endolytic murein transglycosylase |
| RA | 1,282,675 | G→T | G938C (GGT→TGT) | narG → | nitrate reductase A subunit alpha |
| RA | 1,431,511 | G→T | T821T (ACG→ACT) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,456,256 | C→A | P111Q (CCG→CAG) | paaD → | phenylacetate degradation protein |
| RA | 1,526,361 | G→T | A39S (GCT→TCT) | yncG → | putative glutathione S‑transferase YncG |
| RA | 1,609,232 | G→T | C483* (TGC→TGA) | uxaB ← | tagaturonate reductase |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,679,135 | C→A | R237S (CGT→AGT) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,756,181 | G→T | G162C (GGC→TGC) | pykF → | pyruvate kinase I |
| RA | 1,818,174 | A→C | L109L (CTT→CTG) | chbF ← | monoacetylchitobiose‑6‑phosphate hydrolase |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,897,040 | G→T | G37C (GGC→TGC) | sdaA → | L‑serine deaminase I |
| RA | 1,914,320 | C→A | W166L (TGG→TTG) | prc ← | tail‑specific protease |
| RA | 1,928,315 | G→T | P175P (CCC→CCA) | ptrB ← | oligopeptidase B |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,075,017 | G→T | G80V (GGA→GTA) | yeeR → | CP4‑44 prophage; inner membrane protein YeeR |
| RA | 2,166,898 | G→T | E411* (GAA→TAA) | yegQ → | putative peptidase YegQ |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,308,201 | C→A | A139S (GCG→TCG) | yojI ← | ABC transporter family protein/microcin J25 efflux protein |
| RA | 2,334,927 | C→A | W11C (TGG→TGT) | yfaT ← | DUF1175 domain‑containing protein YfaT |
| RA | 2,381,532 | C→A | W4C (TGG→TGT) | elaA ← | putative N‑acetyltransferase ElaA |
| RA | 2,383,905 | C→T | S398F (TCC→TTC) | elaD → | protease ElaD |
| RA | 2,398,560 | C→G | V536L (GTC→CTC) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,409,102 | C→A | P81T (CCG→ACG) | yfbR → | dCMP phosphohydrolase |
| RA | 2,499,397 | G→T | A243S (GCG→TCG) | ypdA → | sensory histidine kinase YpdA |
| RA | 2,633,600 | C→A | E157D (GAG→GAT) | guaB ← | inosine 5'‑monophosphate dehydrogenase |
| RA | 2,642,324 | G→T | P174Q (CCG→CAG) | rodZ ← | transmembrane component of cytoskeleton |
| RA | 2,763,387 | G→T | R52R (CGG→AGG) | abpB ← | CP4‑57 prophage; putative helicase YfjK |
| RA | 2,784,034 | G→C | N132K (AAC→AAG) | ypjB ← | DUF5508 domain‑containing protein YpjB |
| RA | 2,813,588 | G→T | G325C (GGC→TGC) | emrB → | multidrug efflux pump membrane subunit EmrB |
| RA | 2,866,775 | G→T | I259I (ATC→ATA) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,951,184 | G→T | A426A (GCC→GCA) | recD ← | exodeoxyribonuclease V subunit RecD |
| RA | 2,952,872 | G→C | D1044E (GAC→GAG) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 3,077,165 | C→A | G98W (GGG→TGG) | yggP ← | putative zinc‑binding dehydrogenase YggP |
| RA | 3,184,864 | C→A | Q9K (CAA→AAA) | ubiK → | ubiquinone biosynthesis accessory factor UbiK |
| RA | 3,200,146 | G→T | R274S (CGT→AGT) | ygiF ← | inorganic triphosphatase |
| RA | 3,219,859 | C→A | L122L (CTC→CTA) | patA → | putrescine aminotransferase |
| RA | 3,250,224 | C→A | R50S (CGC→AGC) | yqjK → | conserved protein YqjK |
| RA | 3,259,798 | G→T | R105R (CGG→AGG) | tdcF ← | putative enamine/imine deaminase |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,440,769 | C→A | G87G (GGG→GGT) | rpoA ← | RNA polymerase subunit alpha |
| RA | 3,445,101 | G→T | N43K (AAC→AAA) | rpsE ← | 30S ribosomal subunit protein S5 |
| RA | 3,520,495 | G→T | A70E (GCA→GAA) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,719,657 | C→T | V60V (GTC→GTT) | yiaG → | putative DNA‑binding transcriptional regulator YiaG |
| RA | 3,734,171 | G→T | G151V (GGC→GTC) | xylH → | xylose ABC transporter membrane subunit |
| RA | 3,746,598 | C→A | R169S (CGC→AGC) | yiaO → | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ periplasmic binding protein |
| RA | 3,788,823 | G→T | P241P (CCG→CCT) | yibQ → | divergent polysaccharide deacetylase domain‑containing protein YibQ |
| RA | 3,797,530 | C→T | P195S (CCT→TCT) | waaL → | O‑antigen ligase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,929,556 | C→A | E16D (GAG→GAT) | viaA ← | protein ViaA |
| RA | 4,000,241 | G→T | intergenic (+96/+51) | uvrD → / ← yigE | ssDNA translocase and dsDNA helicase ‑ DNA helicase II/DUF2233 domain‑containing protein YigE |
| RA | 4,029,849 | C→A | A375S (GCT→TCT) | fadB ← | dodecenoyl‑CoA delta‑isomerase, enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, 3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,044,135 | G→T | intergenic (+91/‑64) | dsbA → / → yihF | thiol:disulfide oxidoreductase DsbA/uncharacterized protein YihF |
| RA | 4,052,337 | C→A | P98Q (CCG→CAG) | hemN → | coproporphyrinogen III dehydrogenase |
| RA | 4,088,390 | C→A | R489L (CGC→CTC) | frvR ← | putative transcriptional regulator FrvR |
| RA | 4,205,655 | C→A | G93C (GGC→TGC) | purD ← | phosphoribosylamine‑‑glycine ligase |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,266,928 | C→A | intergenic (+67/‑186) | alr → / → tyrB | alanine racemase 1/tyrosine aminotransferase |
| RA | 4,273,990 | C→A | intergenic (‑119/‑135) | uvrA ← / → ssb | excision nuclease subunit A/ssDNA‑binding protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,353,995 | C→A | E241D (GAG→GAT) | lysU ← | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| RA | 4,635,423 | C→A | intergenic (‑113/‑98) | rob ← / → creA | DNA‑binding transcriptional dual regulator Rob/PF05981 family protein CreA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102970 | 3104051 | 1082 | 8 [4] | [5] 8 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423789–3424231 | 3424531–3424240 | 10–743 | 7 [6] | [6] 7 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 26 (0.740) | 11 (0.350) | 10/246 | 1.6 | 29.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 29 (0.930) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 26 (0.740) | 9 (0.290) | 9/246 | 1.8 | 25.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 29 (0.930) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 49 (1.430) | 39/270 | 0.0 | 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 | 3363001 = | 56 (1.590) | 49 (1.400) | 32/276 | 0.1 | 63.4% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 49 (1.390) | 38/278 | 0.0 | 90.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.140) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||