mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 153,654 | A→G | R591R (CGT→CGC) | htrE ← | putative fimbrial usher protein HtrE |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 308,966 | T→C | T123A (ACC→GCC) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 403,332 | A→G | T18A (ACC→GCC) | psiF → | PsiF family protein |
| RA | 418,900 | C→T | H338Y (CAT→TAT) | phoR → | sensory histidine kinase PhoR |
| RA | 602,793 | C→T | P279S (CCG→TCG) | pheP → | phenylalanine:H(+) symporter PheP |
| RA | 621,137 | C→T | A18T (GCC→ACC) | fepG ← | ferric enterobactin ABC transporter membrane subunit FepG |
| RA | 761,033 | G→A | M776I (ATG→ATA) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 823,547 | C→T | A65T (GCG→ACG) | clsB ← | cardiolipin synthase B |
| RA | 837,869 | G→A | G19G (GGC→GGT) | ybiJ ← | DUF1471 domain‑containing protein YbiJ |
| RA | 867,707 | T→C | M63T (ATG→ACG) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 868,422 | (C)8→7 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 956,698 | C→T | intergenic (‑66/‑64) | ycaO ← / → ycaP | ribosomal protein S12 methylthiotransferase accessory factor YcaO/DUF421 domain‑containing protein YcaP |
| RA | 1,077,655 | A→G | C410R (TGC→CGC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,114,775 | (G)5→6 | coding (716/1227 nt) | mdtG ← | efflux pump MdtG |
| RA | 1,118,021 | A→G | R152R (CGT→CGC) | yceI ← | protein YceI |
| RA | 1,165,996 | A→G | intergenic (+311/‑89) | ycfP → / → ndh | UPF0227 protein YcfP/NADH:quinone oxidoreductase II |
| RA | 1,211,925 | T→C | M27V (ATG→GTG) | iraM ← | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,253,492 | A→G | S821P (TCC→CCC) | ycgV ← | putative autotransporter adhesin YcgV |
| RA | 1,323,305 | T→C | V29A (GTG→GCG) | yciV → | RNA/ssDNA 5'‑>3' exonuclease |
| RA | 1,434,409 | A→G | intergenic (‑3/+549) | ynaM ← / ← ttcC | Rac prophage; protein YnaM/putative tRNA 2‑thiocytidine (s(2)C32) synthase |
| RA | 1,479,901 | T→C | L255P (CTG→CCG) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,489,101 | T→C | R290R (CGT→CGC) | aldA → | aldehyde dehydrogenase A |
| RA | 1,507,424 | A→G | H215R (CAT→CGT) | rlhA → | 23S rRNA 5‑hydroxycytidine C2501 synthase |
| RA | 1,541,858 | A→G | Y245H (TAT→CAT) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,545,966 | A→G | A21A (GCT→GCC) | yddL ← | putative uncharacterized protein YddL |
| RA | 1,559,110 | (C)5→6 | coding (801/897 nt) | ddpC ← | putative D,D‑dipeptide ABC transporter membrane subunit DdpC |
| RA | 1,578,224 | A→G | S373S (AGT→AGC) | yddA ← | ABC transporter family protein YddA |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,618,684 | A→C | G75G (GGT→GGG) | marC ← | inner membrane protein MarC |
| JC | 1,619,447 | (TGTGAAC)1→2 | coding (328/435 nt) | marR → | DNA‑binding transcriptional repressor MarR |
| RA | 1,656,986 | T→C | T158A (ACG→GCG) | ynfC ← | UPF0257 family lipoprotein YnfC |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,970,274 | A→G | I237I (ATT→ATC) | tap ← | methyl‑accepting chemotaxis protein Tap |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,016,912 | T→C | V120A (GTT→GCT) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | 2,066,292 | T→C | intergenic (‑528/+13) | cobU ← / ← insH‑6 | cobinamide‑P guanylyltransferase/cobinamide kinase/CP4‑44 prophage; IS5 transposase and trans‑activator |
| RA | 2,139,747 | T→C | intergenic (+262/+12) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,158,392 | T→C | F3L (TTT→CTT) | mdtC → | multidrug efflux pump RND permease subunit MdtC |
| RA | 2,163,822 | T→A | I316N (ATC→AAC) | baeS → | sensory histidine kinase BaeS |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,204,331 | T→C | intergenic (+42/‑265) | yehK → / → yehL | uncharacterized protein YehK/putative AAA(+) MoxR family ATPase YehL |
| RA | 2,222,185 | A→G | M1M (ATG→GTG) † | dld → | D‑lactate dehydrogenase |
| RA | 2,240,766 | T→C | E301E (GAA→GAG) | galS ← | DNA‑binding transcriptional dual regulator GalS |
| RA | 2,297,466 | A→G | V60A (GTT→GCT) | ccmA ← | heme trafficking system ATP‑binding protein |
| RA | 2,640,930 | T→C | E292G (GAA→GGA) | ispG ← | (E)‑4‑hydroxy‑3‑methylbut‑2‑enyl‑diphosphate synthase (flavodoxin) |
| RA | 2,660,486 | G→A | A349V (GCA→GTA) | iscS ← | cysteine desulfurase |
| RA | 2,682,958 | G→A | T32T (ACG→ACA) | yphH → | putative DNA‑binding transcriptional regulator, NAGC‑like |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,778,930 | (C)6→7 | coding (3797/4581 nt) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,795,859 | (A)5→4 | coding (186/663 nt) | csiR → | DNA‑binding transcriptional repressor CsiR |
| RA | 2,857,298 | C→A | A69E (GCG→GAG) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,899,808 | A→G | S156P (TCT→CCT) | ygcW ← | putative deoxygluconate dehydrogenase |
| RA | 3,017,436 | (C)5→4 | coding (1377/3099 nt) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,064,209 | T→C | S73P (TCT→CCT) | scpB → | methylmalonyl‑CoA decarboxylase |
| RA | 3,280,182 | T→C | C423C (TGT→TGC) | kbaZ → | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,441,085 | T→C | E197E (GAA→GAG) | rpsD ← | 30S ribosomal subunit protein S4 |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,601,643 | T→C | A148A (GCA→GCG) | ftsX ← | cell division protein FtsX |
| RA | 3,653,836 | T→C | intergenic (+123/‑125) | yhiS → / → slp | putative uncharacterized protein YhiS/starvation lipoprotein |
| RA | 3,694,108 | A→G | F377L (TTC→CTC) | bcsA ← | cellulose synthase catalytic subunit |
| RA | 3,712,589 | T→C | T116A (ACA→GCA) | yhjY ← | conserved protein YhjY |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,896,997 | A→G | Y75C (TAC→TGC) | yieH → | 6‑phosphogluconate phosphatase |
| RA | 3,913,539 | T→C | T44A (ACC→GCC) | glmS ← | L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,917,535 | A→G | M244T (ATG→ACG) | atpG ← | ATP synthase F1 complex subunit gamma |
| RA | 3,924,178 | T→C | T486A (ACC→GCC) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,972,042 | C→T | G261G (GGC→GGT) | wecC → | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| RA | 3,992,477 | C→T | P442L (CCC→CTC) | cyaA → | adenylate cyclase |
| RA | 4,023,070 | T→C | V112A (GTT→GCT) | tatC → | twin arginine protein translocation system ‑ TatC protein |
| RA | 4,055,309 | T→C | Y344C (TAC→TGC) | glnL ← | sensory histidine kinase NtrB |
| RA | 4,181,664 | T→C | G140G (GGT→GGC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,247,001 | C→A | A73E (GCA→GAA) | malK → | maltose ABC transporter ATP binding subunit |
| RA | 4,255,067 | A→G | V467A (GTC→GCC) | plsB ← | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| RA | 4,259,371 | A→G | E45E (GAA→GAG) | yjbJ → | putative stress response protein |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,265,777 | C→T | intergenic (+48/‑5) | dnaB → / → alr | replicative DNA helicase/alanine racemase 1 |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,522,428 | C→T | G556D (GGC→GAC) | yjhG ← | KpLE2 phage‑like element; D‑xylonate dehydratase |
| RA | 4,560,658 | A→G | V8A (GTA→GCA) | yjiH ← | Gate family protein YjiH |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102965 | 3104069 | 1105 | 26 [25] | [24] 28 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423755–3424233 | 3424531–3424239 | 7–777 | 26 [25] | [25] 31 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 12 (0.140) | 77 (1.020) | 51/244 | 0.2 | 85.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 16 (0.210) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 12 (0.140) | 45 (0.590) | 29/244 | 1.4 | 77.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 16 (0.210) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 63 (0.760) | 40/268 | 0.8 | 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 = | 98 (1.140) | 107 (1.260) | 64/274 | 0.1 | 68.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 83 (0.970) | 49/276 | 0.5 | 95.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||