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 | 67,596 | (T)6→7 | coding (742/1503 nt) | araA ← | L‑arabinose isomerase |
| RA | 156,729 | C→T | G52D (GGT→GAT) | yadN ← | putative fimbrial protein YadN |
| RA | 176,292 | (G)5→6 | coding (1186/1422 nt) | clcA → | chloride:H(+) antiporter ClcA |
| RA | 191,440 | A→G | Y195C (TAC→TGC) | tsf → | protein chain elongation factor EF‑Ts |
| RA | 206,603 | C→T | A493V (GCG→GTG) | dnaE → | DNA polymerase III subunit alpha |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 266,505 | A→G | F17L (TTT→CTT) | yafY ← | CP4‑6 prophage; inner membrane lipoprotein YafY |
| RA | 286,341 | A→G | H316R (CAC→CGC) | yagG → | putative D‑xylonate transporter YagG |
| RA | 303,093 | (G)6→5 | coding (103/615 nt) | yagU → | inner membrane protein that contributes to acid resistance |
| RA | 321,564 | (G)7→8 | intergenic (+483/‑44) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 334,736 | A→G | V96A (GTA→GCA) | yahC ← | uncharacterized protein YahC |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 398,684 | A→G | E271E (GAA→GAG) | yaiW → | surface‑exposed outer membrane lipoprotein |
| RA | 485,347 | (GA)4→3 | coding (272‑273/1194 nt) | acrA ← | multidrug efflux pump membrane fusion lipoprotein AcrA |
| RA | 494,093 | T→C | G6G (GGT→GGC) | ybaB → | putative nucleoid‑associated protein YbaB |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 665,137 | A→G | C18C (TGT→TGC) | rlpA ← | rare lipoprotein RlpA |
| RA | 674,949 | C→T | intergenic (‑166/‑69) | leuS ← / → ybeL | leucine‑‑tRNA ligase/DUF1451 domain‑containing protein YbeL |
| RA | 683,784 | T→C | N210S (AAC→AGC) | rihA ← | pyrimidine‑specific ribonucleoside hydrolase RihA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 894,177 | C→T | P132S (CCC→TCC) | potF → | putrescine ABC transporter periplasmic binding protein |
| RA | 923,487 | A→G | E75G (GAG→GGG) | clpA → | ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,022,692 | A→G | S398P (TCG→CCG) | yccS ← | putative transporter YccS |
| RA | 1,029,739 | (A)8→7 | coding (231/1191 nt) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase |
| RA | 1,035,711 | A→G | T216A (ACC→GCC) | hyaC → | hydrogenase 1 cytochrome b subunit |
| RA | 1,060,354 | A→G | T367A (ACG→GCG) | torA → | trimethylamine N‑oxide reductase 1 |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,164,808 | A→G | E238E (GAA→GAG) | nagZ → | beta‑N‑acetylhexosaminidase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,237,673 | (G)5→6 | coding (103/1299 nt) | dadA → | D‑amino acid dehydrogenase |
| RA | 1,270,999 | A→G | V284A (GTT→GCT) | chaA ← | Na(+)/K(+):H(+) antiporter ChaA |
| RA | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,359,053 | A→G | G45G (GGT→GGC) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,391,837 | A→G | V6A (GTC→GCC) | ycjY ← | putative hydrolase YcjY |
| RA | 1,432,087 | C→T | G1013G (GGC→GGT) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,579,871 | (T)8→9 | coding (920/1158 nt) | ydeM ← | putative anaerobic sulfatase maturation enzyme YdeM |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,612,237 | C→T | C30Y (TGC→TAC) | yneG ← | conserved protein YneG |
| RA | 1,628,934 | G→A | D195N (GAT→AAT) | ydfH → | DNA‑binding transcriptional repressor YdfH |
| RA | 1,632,730 | T→C | intergenic (‑445/‑160) | ydfJ ← / → ynfT | putative transporter YdfJ/Qin prophage; protein YnfT |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,712,518 | (C)6→7 | intergenic (+360/‑251) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,723,936 | T→C | L606L (TTG→CTG) | ydhK → | putative transporter YdhK |
| RA | 1,732,446 | T→C | G1120G (GGT→GGC) | lhr → | putative ATP‑dependent helicase Lhr |
| RA | 1,804,810 | (A)7→8 | pseudogene (1717/1900 nt) | arpB → | putative ankyrin repeat protein B, N‑terminal fragment |
| RA | 1,847,618 | G→A | Q131* (CAG→TAG) | selD ← | selenide, water dikinase |
| 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 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,979,911 | G→A | M53I (ATG→ATA) | uspC → | universal stress protein C |
| RA | 2,026,558 | C→T | G487D (GGC→GAC) | dgcQ ← | putative diguanylate cyclase DgcQ |
| RA | 2,050,863 | A→G | T1976A (ACT→GCT) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,112,376 | T→C | Q229R (CAG→CGG) | rfbB ← | dTDP‑glucose 4,6‑dehydratase 1 |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,176,179 | T→C | N48S (AAC→AGC) | gatZ ← | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatZ |
| RA | 2,252,094 | C→T | A132V (GCC→GTC) | yeiI → | putative sugar kinase YeiI |
| RA | 2,357,149 | A→G | E82E (GAA→GAG) | rpnE → | inactive recombination‑promoting nuclease‑like protein RpnE |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,520,976 | (G)5→6 | noncoding (46/76 nt) | valU → | tRNA‑Val |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,621,890 | T→C | S232P (TCA→CCA) | purM → | phosphoribosylformylglycinamide cyclo‑ligase |
| RA | 2,629,478 | T→C | R63R (CGT→CGC) | yfgG → | protein YfgG |
| RA | 2,641,940 | G→A | A302V (GCC→GTC) | rodZ ← | transmembrane component of cytoskeleton |
| RA | 2,674,415 | G→A | Q92* (CAA→TAA) | yphB ← | putative aldose 1‑epimerase YphB |
| RA | 2,719,472 | T→C | F84L (TTT→CTT) | yfiP → | conserved protein YfiP |
| RA | 2,741,761 | A→G | intergenic (+36/‑114) | yfiL → / → yfiR | DUF2799 domain‑containing lipoprotein YfiL/DUF4154 domain‑containing protein YfiR |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,874,431 | G→A | A330V (GCG→GTG) | cysN ← | sulfate adenylyltransferase subunit 1 |
| RA | 2,935,822 | T→C | V80A (GTA→GCA) | fucI → | L‑fucose isomerase |
| RA | 2,946,181 | A→T | I333N (ATC→AAC) | mltA ← | membrane‑bound lytic murein transglycosylase A |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,970,866 | T→C | G149G (GGT→GGC) | ygdQ → | UPF0053 inner membrane protein YgdQ |
| RA | 2,995,766 | T→C | pseudogene (255/707 nt) | ygeN ← | putative type III secretion system protein |
| RA | 2,996,077 | T→C | pseudogene (284/399 nt) | ygeO ← | putative uncharacterized protein YgeO |
| RA | 3,026,670 | A→G | N302S (AAC→AGC) | guaD → | guanine deaminase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,144,286 | A→G | R285R (CGT→CGC) | hybA ← | hydrogenase 2 iron‑sulfur protein |
| RA | 3,157,607 | T→C | intergenic (+157/‑43) | dkgA → / → yqhG | methylglyoxal reductase DkgA/DUF3828 domain‑containing protein YqhG |
| RA | 3,162,416 | T→C | D85G (GAC→GGC) | ftsP ← | cell division protein required during stress conditions |
| RA | 3,216,481 | (G)6→7 | coding (11/765 nt) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | 3,272,432 | G→A | A107V (GCG→GTG) | garR ← | tartronate semialdehyde reductase |
| RA | 3,286,746 | G→A | L159L (CTG→CTA) | agaI → | putative deaminase AgaI |
| RA | 3,308,219 | T→C | T236A (ACC→GCC) | nlpI ← | lipoprotein NlpI |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,368,754 | A→G | T310A (ACG→GCG) | yhcG → | DUF1016 domain‑containing protein YhcG |
| RA | 3,379,266 | (C)7→6 | coding (732/1128 nt) | zapE ← | cell division factor ZapE with ATPase activity |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,393,494 | T→C | N922S (AAC→AGC) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,441,981 | T→C | N40D (AAC→GAC) | rpsK ← | 30S ribosomal subunit protein S11 |
| RA | 3,460,545 | C→T | H243H (CAC→CAT) | gspF → | Type II secretion system protein GspF |
| RA | 3,507,545 | T→C | N53D (AAT→GAT) | yhfU ← | DUF2620 domain‑containing protein YhfU |
| RA | 3,526,328 | T→C | intergenic (‑179/‑141) | nudE ← / → igaA | ADP‑sugar diphosphatase NudE/inner membrane protein ‑ inhibits the Rcs signaling pathway |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,605,674 | T→C | intergenic (‑64/‑77) | yhhM ← / → yhhN | DUF2500 domain‑containing protein YhhM/conserved inner membrane enzyme YhhN |
| RA | 3,714,680 | T→C | N572S (AAC→AGC) | bisC ← | biotin sulfoxide reductase |
| 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 | 3,885,556 | T→C | F161L (TTT→CTT) | yidC → | membrane protein insertase YidC |
| RA | 3,886,078 | T→C | F335L (TTC→CTC) | yidC → | membrane protein insertase YidC |
| RA | 3,899,468 | G→A | N370N (AAC→AAT) | yieL ← | putative hydrolase YieL |
| RA | 3,907,534 | G→A | N15N (AAC→AAT) | phoU ← | negative regulator of the pho regulon |
| RA | 3,927,933 | C→T | T260M (ACG→ATG) | asnA → | asparagine synthetase A |
| RA | 3,966,860 | A→G | E148E (GAA→GAG) | rho → | transcription termination factor Rho |
| RA | 4,019,249 | A→G | N132S (AAC→AGC) | ubiE → | bifunctional 2‑octaprenyl‑6‑methoxy‑1,4‑benzoquinone methylase and S‑adenosylmethionine:2‑DMK methyltransferase |
| RA | 4,058,270 | A→G | intergenic (‑236/‑137) | glnA ← / → bipA | glutamine synthetase/ribosome‑dependent GTPase, ribosome assembly factor |
| RA | 4,121,744 | A→G | S2P (TCT→CCT) | hslU ← | ATPase component of the HslVU protease |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,336,134 | T→C | T300A (ACG→GCG) | adiC ← | arginine:agmatine antiporter |
| RA | 4,430,909 | C→T | T349M (ACG→ATG) | cycA → | serine/alanine/glycine/cycloserine:H(+)symporter |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,488,579 | (C)7→8 | coding (1485/1503 nt) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,539,616 | C→T | intergenic (‑115/‑1341) | nanC ← / → fimB | N‑acetylneuraminic acid outer membrane channel/regulator for fimA |
| RA | 4,577,854 | A→G | G35G (GGT→GGC) | mcrC ← | 5‑methylcytosine‑specific restriction enzyme subunit McrC |
| RA | 4,606,330 | (G)8→7 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,609,336 | (C)7→8 | intergenic (+13/‑78) | yjjG → / → prfC | pyrimidine nucleotidase/peptide chain release factor RF3 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423782–3424234 | 3424525–3424239 | 6–744 | 13 [12] | [10] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 59 (1.090) | 42/266 | 0.2 | 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 = | 83 (1.490) | 77 (1.390) | 49/272 | 0.1 | 64.9% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 48 (0.860) | 41/274 | 0.2 | 96.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 44 (0.790) | 13 (0.250) | 12/256 | 2.5 | 24.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 38 (0.730) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||