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 | 27,519 | Δ1 bp | coding (227/915 nt) | rihC → | ribonucleoside hydrolase RihC |
| RA | 76,501 | C→T | G267S (GGC→AGC) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 177,992 | A→G | R157R (CGT→CGC) | btuF ← | vitamin B12 ABC transporter periplasmic binding protein |
| RA | 208,270 | A→G | I1049V (ATC→GTC) | dnaE → | DNA polymerase III subunit alpha |
| RA | 213,589 | A→G | E420G (GAG→GGG) | tilS → | tRNA(Ile)‑lysidine synthetase |
| RA | 225,800 | A→G | noncoding (42/2904 nt) | rrlH → | 23S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 258,897 | A→G | pseudogene (222/331 nt) | crl → | RNA polymerase holoenzyme assembly factor Crl |
| RA | 281,679 | T→C | D102G (GAC→GGC) | yagA ← | CP4‑6 prophage; integrase core domain‑containing protein YagA |
| RA | 310,347 | C→T | V109M (GTG→ATG) | ecpA ← | common pilus major subunit |
| RA | 375,596 | A→G | A46A (GCA→GCG) | mhpT → | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 427,480 | A→G | N65S (AAC→AGC) | yajC → | Sec translocon accessory complex subunit YajC |
| RA | 522,295 | C→T | A627V (GCA→GTA) | ybbP → | putative ABC transporter membrane subunit YbbP |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 556,864 | A→G | F4L (TTT→CTT) | ybcJ ← | putative RNA‑binding protein YbcJ |
| RA | 564,105 | (A)6→5 | coding (376/633 nt) | fimZ ← | putative LuxR family transcriptional regulator FimZ |
| RA | 571,607 | G→A | D52N (GAT→AAT) | ybcM → | DLP12 prophage; putative DNA‑binding transcriptional regulator |
| RA | 571,977 | C→T | P175L (CCC→CTC) | ybcM → | DLP12 prophage; putative DNA‑binding transcriptional regulator |
| RA | 630,361 | G→A | G156G (GGG→GGA) | cstA → | carbon starvation protein A |
| RA | 658,579 | T→C | pseudogene (549/788 nt) | ybeM → | deamidated glutathione amidase, N‑terminal fragment |
| RA | 684,726 | T→C | D177G (GAC→GGC) | gltL ← | glutamate/aspartate ABC transporter ATP binding subunit |
| RA | 719,001 | T→C | N487S (AAT→AGT) | speF ← | ornithine decarboxylase, degradative |
| RA | 744,027 | A→G | Q145Q (CAA→CAG) | pxpB → | 5‑oxoprolinase component B |
| RA | 764,071 | A→G | N353S (AAC→AGC) | sucC → | succinyl‑CoA synthetase subunit beta |
| RA | 798,972 | C→T | C129C (TGC→TGT) | pgl → | 6‑phosphogluconolactonase |
| RA | 804,101 | C→T | P200L (CCA→CTA) | ybhJ → | putative hydratase YbhJ |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 984,199 | (G)5→6 | coding (550/648 nt) | gloC → | hydroxyacylglutathione hydrolase GloC |
| RA | 986,851 | (A)5→4 | coding (132/1089 nt) | ompF ← | outer membrane porin F |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,085,233 | C→T | A81V (GCG→GTG) | phoH → | ATP‑binding protein PhoH |
| RA | 1,096,988 | (A)8→7 | intergenic (+159/+577) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,110,436 | A→G | T368A (ACG→GCG) | opgG → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein G |
| RA | 1,112,995 | A→G | K711K (AAA→AAG) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| RA | 1,131,170 | (A)6→7 | coding (153/417 nt) | flgB → | flagellar basal‑body rod protein FlgB |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,159,182 | C→T | A438A (GCC→GCT) | ptsG → | glucose‑specific PTS enzyme IIBC component |
| RA | 1,177,383 | A→G | M22V (ATG→GTG) | lolE → | lipoprotein release complex ‑ inner membrane subunit |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,226,800 | A→G | L67L (TTA→TTG) | ycgJ → | PF05666 family protein YcgJ |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,371,403 | T→G | S396R (AGT→AGG) | ycjM → | glucosylglycerate phosphorylase |
| RA | 1,401,562 | A→G | V71A (GTG→GCG) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
| RA | 1,488,054 | C→T | intergenic (+19/‑178) | ydcF → / → aldA | DUF218 domain‑containing protein YdcF/aldehyde dehydrogenase A |
| RA | 1,539,139 | C→T | S1151N (AGC→AAC) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,542,486 | G→A | S35S (AGC→AGT) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,680,640 | G→A | A362T (GCC→ACC) | ydgI → | putative arginine:ornithine antiporter |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,784,530 | T→C | R518R (CGT→CGC) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,978,173 | G→A | H9Y (CAC→TAC) | flhD ← | DNA‑binding transcriptional dual regulator FlhD |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,201,201 | T→C | V308A (GTC→GCC) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,216,779 | T→C | H210R (CAC→CGC) | yehX ← | glycine betaine ABC transporter ATP binding subunit YehX |
| RA | 2,249,802 | T→C | V29A (GTC→GCC) | yeiH → | conserved inner membrane protein YeiH |
| RA | 2,252,235 | A→G | N179S (AAC→AGC) | yeiI → | putative sugar kinase YeiI |
| RA | 2,258,987 | T→C | T104A (ACC→GCC) | psuK ← | putative pseudouridine kinase |
| RA | 2,319,449 | T→C | N143S (AAC→AGC) | rcsC ← | sensory histidine kinase RcsC |
| RA | 2,347,256 | A→G | intergenic (+106/‑128) | nrdA → / → nrdB | ribonucleoside‑diphosphate reductase 1 subunit alpha/ribonucleoside‑diphosphate reductase 1 subunit beta |
| RA | 2,347,261 | G→A | intergenic (+111/‑123) | nrdA → / → nrdB | ribonucleoside‑diphosphate reductase 1 subunit alpha/ribonucleoside‑diphosphate reductase 1 subunit beta |
| RA | 2,347,288 | Δ1 bp | intergenic (+138/‑96) | nrdA → / → nrdB | ribonucleoside‑diphosphate reductase 1 subunit alpha/ribonucleoside‑diphosphate reductase 1 subunit beta |
| RA | 2,377,690 | C→T | A524T (GCC→ACC) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase |
| RA | 2,426,793 | T→C | intergenic (‑5/+216) | hisJ ← / ← argT | histidine ABC transporter periplasmic binding protein/lysine/arginine/ornithine ABC transporter periplasmic binding protein |
| RA | 2,443,240 | G→A | A493T (GCA→ACA) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,454,909 | G→A | pseudogene (93/2646 nt) | yfcU ← | putative outer membrane usher protein YfcU |
| RA | 2,507,579 | A→G | L106L (TTG→CTG) | fryC ← | putative PTS enzyme IIC component FryC |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,564,444 | T→C | intergenic (+72/‑79) | yffR → / → yffS | CPZ‑55 prophage; uncharacterized protein YffR/CPZ‑55 prophage; uncharacterized protein YffS |
| RA | 2,599,252 | A→G | V170A (GTA→GCA) | dapA ← | 4‑hydroxy‑tetrahydrodipicolinate synthase |
| RA | 2,657,759 | G→A | P393S (CCA→TCA) | hscA ← | iron‑sulfur cluster biosynthesis chaperone HscA |
| RA | 2,678,790 | G→A | A193V (GCG→GTG) | yphF ← | putative ABC transporter periplasmic binding protein YphF |
| RA | 2,719,629 | T→C | L136P (CTC→CCC) | yfiP → | conserved protein YfiP |
| RA | 2,793,987 | G→A | S418N (AGC→AAC) | gabT → | 4‑aminobutyrate aminotransferase GabT |
| RA | 2,805,945 | A→G | Q377Q (CAA→CAG) | proV → | glycine betaine ABC transporter ATP binding subunit ProV |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,821,486 | T→C | T176A (ACT→GCT) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 2,826,079 | T→C | M83T (ATG→ACG) | srlA → | sorbitol‑specific PTS enzyme IIC2 component |
| RA | 2,829,459 | T→C | I138T (ATC→ACC) | srlR → | DNA‑binding transcriptional repressor SrlR |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,859,789 | T→C | N10N (AAT→AAC) | pphB → | phosphoprotein phosphatase 2 |
| RA | 2,890,403 | T→C | Q499R (CAG→CGG) | cysJ ← | sulfite reductase, flavoprotein subunit |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,988,156 | G→A | S207S (TCG→TCA) | yqeH → | putative LuxR family transcriptional regulator YqeH |
| RA | 3,013,075 | G→A | P389S (CCG→TCG) | yqeB ← | XdhC‑CoxI family protein YqeB |
| RA | 3,066,383 | T→C | H264R (CAC→CGC) | ygfI ← | putative LysR‑type DNA‑binding transcriptional regulator YgfI |
| RA | 3,067,741 | T→C | T114A (ACG→GCG) | yggE ← | uncharacterized protein YggE |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,097,958 | C→T | A231V (GCG→GTG) | yggW → | putative coproporphyrinogen‑III oxidase‑like protein YggW |
| RA | 3,158,512 | G→A | R288H (CGC→CAC) | yqhG → | DUF3828 domain‑containing protein YqhG |
| RA | 3,233,830 | A→G | S105S (TCT→TCC) | higA ← | antitoxin/DNA‑binding transcriptional repressor HigA |
| RA | 3,283,280 | C→T | I46I (ATC→ATT) | kbaY → | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaY |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,418,981 | A→G | intergenic (+370/‑61) | yhdV → / → yhdW | lipoprotein YhdV/putative ABC transporter periplasmic binding protein YhdW |
| RA | 3,446,881 | C→T | A2T (GCT→ACT) | rpsN ← | 30S ribosomal subunit protein S14 |
| RA | 3,475,659 | Δ1 bp | coding (60/387 nt) | tusD ← | sulfurtransferase complex subunit TusD |
| RA | 3,498,269 | C→T | P148S (CCG→TCG) | cysG → | siroheme synthase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,622,701 | T→C | Y1170Y (TAT→TAC) | rhsB → | rhs element protein RhsB |
| RA | 3,698,498 | T→C | G95G (GGT→GGC) | bcsG → | cellulose phosphoethanolamine transferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,905,639 | (A)9→8 | intergenic (‑42/+92) | bglF ← / ← bglG | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase/transcriptional antiterminator BglG |
| RA | 3,930,387 | C→T | R236H (CGC→CAC) | ravA ← | regulatory ATPase RavA |
| RA | 4,008,417 | A→G | intergenic (+40/+22) | rhtC → / ← rhtB | L‑threonine exporter/L‑homoserine/L‑homoserine lactone/L‑threonine exporter |
| RA | 4,027,325 | C→T | intergenic (+97/+284) | fre → / ← fadA | flavin reductase/3‑ketoacyl‑CoA thiolase |
| RA | 4,101,899 | A→G | V70V (GTA→GTG) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,181,411 | T→C | V56A (GTA→GCA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,346,676 | A→G | R217R (CGT→CGC) | fumB ← | fumarase B |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,554,639 | A→G | I22V (ATC→GTC) | uxuR → | DNA‑binding transcriptional repressor UxuR |
| RA | 4,564,136 | A→G | V185A (GTG→GCG) | yjiL ← | putative ATPase, activator of (R)‑hydroxyglutaryl‑CoA dehdratase |
| RA | 4,611,779 | G→A | S128S (TCG→TCA) | osmY → | periplasmic chaperone OsmY |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2304631–2304796 | 2304962–2304802 | 7–332 | 17 [16] | [16] 24 | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | * | ÷ | NC_000913 | 3423753–3424234 | 3424528–3424238 | 5–776 | 18 [16] | [16] 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 = | 9 (0.130) | 79 (1.290) | 49/244 | 0.1 | 91.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 7 (0.110) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 9 (0.130) | 66 (1.080) | 42/244 | 0.3 | 89.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 7 (0.110) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 133 (1.920) | 97 (1.410) | 56/274 | 0.1 | 59.0% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 77 (1.110) | 54/276 | 0.1 | 96.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||