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 | 57,230 | A→G | intergenic (‑121/‑134) | lptD ← / → djlA | lipopolysaccharide assembly protein LptD/co‑chaperone protein DjlA |
| RA | 78,635 | G→A | A339T (GCA→ACA) | setA → | sugar exporter SetA |
| RA | 94,115 | C→T | A317V (GCG→GTG) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 125,335 | A→G | E773E (GAA→GAG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 140,126 | C→T | G367D (GGT→GAT) | gcd ← | quinoprotein glucose dehydrogenase |
| RA | 163,804 | T→C | V567A (GTA→GCA) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
| RA | 164,959 | C→T | A77V (GCC→GTC) | mrcB → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| RA | 205,795 | A→G | T224A (ACC→GCC) | dnaE → | DNA polymerase III subunit alpha |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 408,431 | A→G | E85E (GAA→GAG) | ppnP → | nucleoside phosphorylase PpnP |
| RA | 427,675 | A→G | Y10C (TAC→TGC) | secD → | Sec translocon accessory complex subunit SecD |
| RA | 477,636 | T→C | T328A (ACG→GCG) | pdeB ← | c‑di‑GMP phosphodiesterase PdeB |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 528,172 | (G)6→5 | pseudogene (224/711 nt) | ylbH → | putative RHS domain‑containing protein YlbH |
| RA | 596,207 | A→G | Q203R (CAA→CGA) | cusC → | copper/silver export system outer membrane channel |
| RA | 637,533 | T→C | K29R (AAA→AGA) | ybdO ← | putative LysR family DNA‑binding transcriptional regulator YbdO |
| RA | 653,178 | C→T | A315V (GCC→GTC) | dpiB → | sensory histidine kinase DpiB |
| RA | 672,766 | A→G | V673A (GTC→GCC) | leuS ← | leucine‑‑tRNA ligase |
| RA | 765,211 | G→A | A222V (GCT→GTT) | mngR ← | DNA‑binding transcriptional repressor MngR |
| RA | 786,694 | Δ1 bp | intergenic (+9/+149) | aroG → / ← gpmA | 3‑deoxy‑7‑phosphoheptulonate synthase, Phe‑sensitive/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| RA | 808,256 | T→C | Q334Q (CAA→CAG) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 830,184 | C→T | A154T (GCC→ACC) | cecR ← | DNA‑binding transcriptional dual regulator CecR |
| RA | 840,470 | G→A | S354S (AGC→AGT) | fiu ← | putative iron siderophore outer membrane transporter |
| RA | 864,955 | T→C | T59A (ACG→GCG) | moeB ← | molybdopterin‑synthase adenylyltransferase |
| RA | 868,422 | (C)8→9 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 885,305 | T→C | intergenic (‑75/+11) | ybjH ← / ← ybjI | uncharacterized protein YbjH/5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 902,735 | A→G | M85T (ATG→ACG) | artI ← | putative ABC transporter periplasmic binding protein ArtI |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 953,662 | A→G | L269L (TTG→CTG) | focA ← | formate channel FocA |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,045,014 | C→T | G264S (GGT→AGT) | gfcE ← | putative exopolysaccharide export lipoprotein GfcE |
| RA | 1,055,678 | T→C | G167G (GGA→GGG) | torS ← | sensory histidine kinase TorS |
| RA | 1,062,967 | A→G | V270A (GTA→GCA) | cbpA ← | curved DNA‑binding protein |
| RA | 1,135,663 | (G)5→6 | coding (100/699 nt) | flgH → | flagellar L‑ring protein |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,152,649 | T→C | G237G (GGT→GGC) | fabF → | beta‑ketoacyl‑[acyl carrier protein] synthase II |
| RA | 1,153,578 | C→T | S93S (AGC→AGT) | pabC → | aminodeoxychorismate lyase |
| RA | 1,208,928 | A→G | R64R (CGT→CGC) | tfaE ← | e14 prophage; putative tail fiber assembly protein TfaE |
| RA | 1,215,783 | C→T | intergenic (‑308/‑6) | bluF ← / → ycgZ | blue light‑responsive regulator of BluR/putative two‑component system connector protein YcgZ |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,246,801 | A→G | G192G (GGT→GGC) | treA ← | periplasmic trehalase |
| RA | 1,391,724 | (C)5→6 | coding (130/921 nt) | ycjY ← | putative hydrolase YcjY |
| RA | 1,480,925 | G→A | G6D (GGC→GAC) | ynbD → | putative phosphatase |
| RA | 1,540,626 | T→C | L655L (CTA→CTG) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,256 | (C)8→7 | pseudogene (3831/5422 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 | 1,685,542 | (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 | 1,810,896 | T→C | intergenic (+95/‑38) | ydjM → / → tcyP | putative inner membrane protein regulated by LexA/cystine/sulfocysteine:cation symporter |
| RA | 1,843,294 | A→G | Q308Q (CAA→CAG) | gdhA → | glutamate dehydrogenase |
| RA | 1,861,001 | T→C | N111S (AAC→AGC) | ydjL ← | putative zinc‑binding dehydrogenase YdjL |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,879,362 | (T)8→9 | intergenic (‑107/+41) | yeaQ ← / ← yoaG | PF04226 family protein YeaQ/DUF1869 domain‑containing protein YoaG |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,895,043 | T→C | L80P (CTA→CCA) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,910,536 | T→C | G87G (GGT→GGC) | yebQ → | putative transporter YebQ |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,010,684 | T→C | S29P (TCT→CCT) | yedL → | putative acetyltransferase YedL |
| RA | 2,111,526 | T→C | T151A (ACC→GCC) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,139,283 | T→C | V461A (GTG→GCG) | yegH → | inner membrane protein YegH |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,191,241 | A→G | G135G (GGT→GGC) | yehC ← | putative fimbrial chaperone YehC |
| RA | 2,215,832 | (C)5→4 | coding (645/732 nt) | yehW ← | glycine betaine ABC transporter membrane subunit YehW |
| RA | 2,224,977 | A→G | intergenic (‑107/+67) | pbpG ← / ← yohC | peptidoglycan DD‑endopeptidase PbpG/putative inner membrane protein |
| RA | 2,231,757 | T→C | intergenic (+43/‑87) | yohK → / → cdd | PF04712 family membrane protein YohK/cytidine/deoxycytidine deaminase |
| RA | 2,256,315 | A→G | Y341H (TAC→CAC) | psuT ← | putative pseudouridine transporter |
| RA | 2,256,899 | G→A | A146V (GCG→GTG) | psuT ← | putative pseudouridine transporter |
| RA | 2,337,269 | T→C | T718A (ACC→GCC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,454,607 | A→T | pseudogene (395/2646 nt) | yfcU ← | putative outer membrane usher protein YfcU |
| RA | 2,493,138 | G→A | P39P (CCC→CCT) | frc ← | formyl‑CoA transferase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,538,974 | T→C | S204G (AGC→GGC) | cysM ← | cysteine synthase B |
| RA | 2,626,105 | G→A | E331K (GAA→AAA) | ppx → | exopolyphosphatase |
| RA | 2,626,342 | C→T | R410C (CGC→TGC) | ppx → | exopolyphosphatase |
| RA | 2,681,049 | T→C | N566S (AAC→AGC) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,753,046 | A→G | T418A (ACC→GCC) | recN → | DNA repair protein RecN |
| RA | 2,765,794 | (C)7→8 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,767,507 | (C)7→8 | intergenic (+152/‑203) | rnlB → / → yfjP | CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP |
| RA | 2,777,841 | A→G | intergenic (+59/+305) | ypjF → / ← ypjA | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,820,068 | C→T | K648K (AAG→AAA) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 2,829,213 | T→C | V56A (GTG→GCG) | srlR → | DNA‑binding transcriptional repressor SrlR |
| RA | 2,855,402 | T→C | R355R (CGT→CGC) | fhlA → | DNA‑binding transcriptional activator FhlA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,015,001 | A→G | R19R (CGT→CGC) | yqeC ← | uncharacterized protein YqeC |
| RA | 3,057,148 | A→G | intergenic (+157/+30) | sibC → / ← serA | small RNA SibC/phosphoglycerate dehydrogenase |
| RA | 3,059,395 | C→T | pseudogene (217/231 nt) | yqfE ← | conserved protein YqfE |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,109,589 | T→C | L13L (TTA→CTA) | yqgA → | DUF554 domain‑containing protein YqgA |
| RA | 3,114,688 | (C)5→6 | coding (4425/4563 nt) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,147,743 | T→C | intergenic (‑3/‑154) | yqhI ← / → gpr | protein YqhI/L‑glyceraldehyde 3‑phosphate reductase |
| RA | 3,150,856 | T→C | I130V (ATA→GTA) | exbD ← | Ton complex subunit ExbD |
| RA | 3,151,829 | C→T | K52K (AAG→AAA) | exbB ← | Ton complex subunit ExbB |
| RA | 3,167,837 | (C)5→6 | intergenic (‑119/+14) | ygiS ← / ← mqsA | putative deoxycholate binding periplasmic protein/antitoxin of the MqsRA toxin‑antitoxin system/DNA‑binding transcriptional repressor MqsA |
| RA | 3,179,724 | A→G | P43P (CCA→CCG) | ygiA → | putative protein YgiA |
| RA | 3,208,696 | G→A | A225T (GCA→ACA) | ttdT → | L‑tartrate:succinate antiporter |
| RA | 3,250,291 | T→C | V72A (GTC→GCC) | yqjK → | conserved protein YqjK |
| RA | 3,298,612 | T→C | S79G (AGC→GGC) | yraR ← | putative nucleoside‑diphosphate‑sugar epimerase |
| RA | 3,318,699 | T→C | G21G (GGT→GGC) | argG → | argininosuccinate synthetase |
| RA | 3,326,663 | T→C | E91E (GAA→GAG) | ftsH ← | ATP‑dependent zinc metalloprotease FtsH |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,362,708 | T→C | A199A (GCT→GCC) | yhcA → | putative fimbrial chaperone YhcA |
| RA | 3,376,277 | T→C | intergenic (+41/+2) | dcuD → / ← sspB | putative transporter DcuD/ClpXP protease specificity‑enhancing factor |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,469,775 | C→T | A27T (GCA→ACA) | chiA ← | endochitinase |
| RA | 3,473,693 | T→C | N130S (AAC→AGC) | rpsG ← | 30S ribosomal subunit protein S7 |
| RA | 3,477,486 | T→C | intergenic (‑67/‑154) | fkpA ← / → slyX | peptidyl‑prolyl cis‑trans isomerase FkpA/protein SlyX |
| RA | 3,479,075 | C→T | G511G (GGG→GGA) | kefB ← | K(+) : H(+) antiporter KefB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,564,496 | T→C | T696A (ACA→GCA) | glgP ← | glycogen phosphorylase |
| RA | 3,580,930 | (A)9→8 | noncoding (87/90 nt) | ryhB ← | small regulatory RNA RyhB |
| RA | 3,591,868 | T→C | D153G (GAC→GGC) | ugpB ← | sn‑glycerol 3‑phosphate ABC transporter periplasmic binding protein |
| RA | 3,625,677 | A→G | intergenic (+163/+2) | yhhI → / ← yhhJ | putative transposase/ABC transporter family protein YhhJ |
| RA | 3,728,118 | (C)8→9 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,817,594 | A→G | intergenic (+55/‑166) | yicC → / → dinD | UPF0701 family protein YicC/DNA damage‑inducible protein D |
| RA | 3,846,693 | T→C | T159A (ACA→GCA) | uhpT ← | hexose‑6‑phosphate:phosphate antiporter |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,912,976 | T→C | K231K (AAA→AAG) | glmS ← | L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,944,114 | (G)6→7 | noncoding (411/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 4,078,312 | A→G | A288A (GCA→GCG) | yiiD → | putative acetyltransferase YiiD |
| RA | 4,106,950 | A→G | N161S (AAC→AGC) | fieF → | Zn(2(+))/Fe(2(+))/Cd(2(+)) exporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,318,226 | A→G | V180A (GTG→GCG) | phnK ← | carbon‑phosphorus lyase subunit PhnK |
| RA | 4,444,104 | C→T | P575S (CCA→TCA) | tamA → | translocation and assembly module subunit TamA |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,453,103 | T→C | L178P (CTG→CCG) | ytfT → | galactofuranose ABC transporter putative membrane subunit YtfT |
| RA | 4,464,379 | C→T | A111T (GCC→ACC) | treC ← | trehalose‑6‑phosphate hydrolase |
| RA | 4,485,828 | A→G | Y42H (TAC→CAC) | pepA ← | aminopeptidase A/I |
| RA | 4,582,590 | A→G | R153R (CGT→CGC) | hsdM ← | type I restriction enzyme EcoKI methyltransferase component |
| RA | 4,594,568 | A→G | V52A (GTA→GCA) | lgoT ← | galactonate:H(+) symporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 79886 | 79890 | 5 | 5 [0] | [2] 4 | leuC | 3‑isopropylmalate dehydratase subunit LeuC |
| * | * | ÷ | NC_000913 | 729903–730133 | 730181–730147 | 15–279 | 3 [2] | [2] 4 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 2629649 | 2629721 | 73 | 4 [1] | [2] 3 | yfgG/yfgH | protein YfgG/lipoprotein YfgH |
| * | * | ÷ | NC_000913 | 3423795–3424232 | 3424523–3424242 | 11–729 | 3 [1] | [1] 3 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3751946 | 3751983 | 38 | 3 [1] | [2] 3 | yiaT/yiaU | outer membrane protein YiaT/putative LysR‑type DNA‑binding transcriptional regulator YiaU |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 6 (0.260) | 26 (1.260) | 20/244 | 0.2 | 78.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 9 (0.440) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.260) | 19 (0.920) | 16/244 | 0.3 | 72.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 9 (0.440) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 26 (1.150) | 22/268 | 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 = | 31 (1.330) | 23 (0.990) | 20/274 | 0.2 | 59.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 24 (1.030) | 20/276 | 0.2 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||