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 | 14,618 | G→A | G151S (GGT→AGT) | dnaJ → | chaperone protein DnaJ |
| RA | 213,774 | G→A | V53V (GTC→GTT) | rof ← | modulator of Rho‑dependent transcription termination |
| RA | 247,671 | (G)6→7 | coding (35/498 nt) | rayT → | REP‑associated tyrosine transposase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 282,018 | C→G | intergenic (‑35/‑260) | yagA ← / → yagE | CP4‑6 prophage; integrase core domain‑containing protein YagA/CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase |
| RA | 330,809 | G→A | W449* (TGG→TGA) | betT → | choline:H(+) symporter |
| RA | 352,901 | C→T | P66S (CCA→TCA) | prpE → | propionyl‑CoA synthetase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 426,394 | C→T | I86I (ATC→ATT) | tgt → | tRNA‑guanine transglycosylase |
| RA | 464,662 | C→T | S87S (AGC→AGT) | fadM → | thioesterase III |
| RA | 502,939 | C→T | T100T (ACG→ACA) | ybaL ← | putative transporter YbaL |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 535,874 | A→G | E55E (GAA→GAG) | hyi → | hydroxypyruvate isomerase |
| RA | 537,458 | G→A | L291L (CTG→CTA) | glxR → | tartronate semialdehyde reductase 2 |
| RA | 637,839 | C→T | M245I (ATG→ATA) | dsbG ← | protein sulfenic acid reductase DsbG |
| RA | 702,660 | A→G | V31A (GTC→GCC) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| 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 | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,044,448 | C→T | A77T (GCA→ACA) | etp ← | phosphotyrosine‑protein phosphatase |
| RA | 1,121,588 | T→C | E340E (GAA→GAG) | pyrC ← | dihydroorotase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,236,717 | C→T | S175S (TCG→TCA) | ycgB ← | PF04293 family protein YcgB |
| RA | 1,276,665 | G→A | R318R (CGC→CGT) | narX ← | sensory histidine kinase NarX |
| RA | 1,293,529 | G→A | M1M (ATG→ATA) † | tdk → | thymidine/deoxyuridine kinase |
| RA | 1,322,614 | C→T | L111L (CTG→CTA) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,342,977 | G→A | G107D (GGC→GAC) | yciH → | putative translation factor |
| RA | 1,428,487 | G→A | A80A (GCC→GCT) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,428,499 | G→C | A76A (GCC→GCG) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,428,652 | G→C | L25M (CTC→TTG) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,428,654 | G→A | L25M (CTC→TTG) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,430,995 | G→A | L649L (CTG→CTA) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,448,217 | C→T | C233C (TGC→TGT) | feaB → | phenylacetaldehyde dehydrogenase |
| RA | 1,471,131 | A→G | pseudogene (613/3495 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,497,591 | T→C | F246L (TTC→CTC) | opgD → | glucan biosynthesis protein D |
| RA | 1,518,562 | A→G | G95G (GGT→GGC) | mnaT ← | L‑amino acid N‑acyltransferase |
| RA | 1,518,750 | T→C | T33A (ACG→GCG) | mnaT ← | L‑amino acid N‑acyltransferase |
| 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 | 1,767,595 | C→T | R364Q (CGG→CAG) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,767,977 | G→A | R237C (CGC→TGC) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,769,302 | G→A | V77M (GTG→ATG) | ydiK → | putative transporter YdiK |
| RA | 1,800,787 | A→G | V595A (GTC→GCC) | thrS ← | threonine‑‑tRNA ligase |
| RA | 1,863,367 | C→T | G199G (GGC→GGT) | gapA → | glyceraldehyde‑3‑phosphate dehydrogenase A |
| 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 | 1,907,400 | G→A | N12N (AAC→AAT) | cspC ← | stress protein, member of the CspA family |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,067,300 | C→T | G8R (GGA→AGA) | insH‑6 ← | CP4‑44 prophage; IS5 transposase and trans‑activator |
| RA | 2,070,839 | T→C | pseudogene (54/426 nt) | yeeP → | CP4‑44 prophage; putative GTP‑binding protein |
| RA | 2,081,197 | C→T | W22* (TGG→TGA) | sbmC ← | DNA gyrase inhibitor |
| RA | 2,084,240 | C→T | V72I (GTT→ATT) | yeeD ← | putative sulfurtransferase YeeD |
| RA | 2,103,089 | T→C | pseudogene (301/446 nt) | wbbL ← | interrupted rhamnosyltransferase WbbL |
| RA | 2,152,793 | A→G | R112R (CGT→CGC) | yegL ← | IPR002035 domain‑containing protein YegL |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,178,107 | A→G | V153A (GTG→GCG) | fbaB ← | fructose‑bisphosphate aldolase class I |
| RA | 2,190,941 | A→G | I235I (ATT→ATC) | yehC ← | putative fimbrial chaperone YehC |
| RA | 2,194,172 | G→A | intergenic (‑4/‑128) | mrp ← / → metG | P‑loop NTPase family protein/methionine‑‑tRNA ligase |
| RA | 2,296,418 | T→C | T203A (ACC→GCC) | ccmB ← | heme trafficking system membrane protein CcmB |
| RA | 2,425,983 | G→A | intergenic (‑67/+23) | hisQ ← / ← hisJ | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisQ/histidine ABC transporter periplasmic binding protein |
| RA | 2,429,280 | G→A | P320L (CCG→CTG) | purF ← | amidophosphoribosyltransferase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,490,692 | +C | coding (1259/1695 nt) | oxc ← | oxalyl‑CoA decarboxylase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,562,631 | T→C | R36R (CGT→CGC) | yffP → | CPZ‑55 prophage; uncharacterized protein YffP |
| RA | 2,565,631 | G→A | G418G (GGC→GGT) | eutA ← | reactivating factor for ethanolamine ammonia‑lyase EutBC |
| RA | 2,589,447 | (G)5→6 | coding (1853/3114 nt) | acrD → | multidrug efflux pump RND permease AcrD |
| RA | 2,644,687 | A→G | F60L (TTT→CTT) | ndk ← | nucleoside diphosphate kinase |
| RA | 2,688,887 | +G | coding (620/714 nt) | qseG ← | outer membrane lipoprotein QseG |
| RA | 2,708,278 | C→T | W159* (TGG→TGA) | rseB ← | anti‑sigma factor stabilizing protein RseB |
| RA | 2,767,432 | G→A | intergenic (+77/‑278) | rnlB → / → yfjP | CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,811,933 | T→C | S169S (AGT→AGC) | emrA → | multidrug efflux pump membrane fusion protein EmrA |
| RA | 2,819,492 | G→A | G840G (GGC→GGT) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 2,855,738 | T→C | G467G (GGT→GGC) | 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 | 2,908,900 | A→G | L256P (CTG→CCG) | pyrG ← | CTP synthetase |
| RA | 2,941,643 | A→G | intergenic (‑12/+7) | ygdD ← / ← gcvA | conserved inner membrane protein YgdD/DNA‑binding transcriptional dual regulator GcvA |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,994,202 | (A)7→6 | pseudogene (264/503 nt) | pbl → | transglycosylase domain‑containing protein Pbl |
| RA | 3,008,079 | G→A | T190T (ACG→ACA) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,071,327 | A→G | intergenic (‑83/+132) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase class II/phosphoglycerate kinase |
| RA | 3,103,609 | T→C | C199C (TGT→TGC) | mutY → | adenine DNA glycosylase |
| RA | 3,159,844 | G→A | P435S (CCA→TCA) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,186,207 | G→A | P7P (CCG→CCA) | insC‑5 → | IS2 insertion element repressor InsA |
| RA | 3,246,636 | C→T | intergenic (+114/‑16) | exuT → / → exuR | hexuronate transporter/DNA‑binding transcriptional repressor ExuR |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,385,668 | G→A | G44D (GGT→GAT) | yhcN → | DUF1471 domain‑containing stress‑induced protein YhcN |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,411,171 | C→T | R298C (CGC→TGC) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | 3,474,817 | (G)5→4 | coding (149/288 nt) | tusB ← | sulfurtransferase complex subunit TusB |
| RA | 3,513,894 | (T)6→7 | coding (496/759 nt) | gph ← | phosphoglycolate phosphatase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,576,957 | C→T | V35V (GTG→GTA) | gntU ← | low‑affinity gluconate transporter |
| RA | 3,729,268 | C→T | R35H (CGC→CAC) | xylB ← | xylulokinase |
| RA | 3,762,118 | T→C | intergenic (‑163/‑65) | yibF ← / → rhsA | glutathione transferase‑like protein YibF/rhs element protein RhsA |
| RA | 3,765,830 | G→A | R1216R (CGG→CGA) | rhsA → | rhs element protein RhsA |
| RA | 3,767,469 | T→C | pseudogene (249/702 nt) | yibJ → | putative RHS domain‑containing protein YibJ |
| 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 | 3,881,536 | C→T | L262L (CTG→CTA) | dnaN ← | beta sliding clamp |
| RA | 3,925,705 | G→A | intergenic (‑72/+307) | mnmG ← / ← mioC | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG/flavoprotein MioC |
| RA | 3,929,287 | C→T | W106* (TGG→TAG) | viaA ← | protein ViaA |
| RA | 4,083,237 | C→T | P862P (CCG→CCA) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,325,607 | G→A | A45A (GCC→GCT) | yjdN ← | conserved protein YjdN |
| RA | 4,375,940 | T→C | F81S (TTC→TCC) | efp → | protein chain elongation factor EF‑P |
| RA | 4,379,075 | T→C | K98E (AAA→GAA) | frdD ← | fumarate reductase membrane protein FrdD |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,510,363 | (C)6→7 | intergenic (+230/+327) | yjhV → / ← fecE | KpLE2 phage‑like element; putative uncharacterized protein YjhV/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,585,748 | G→A | F338F (TTC→TTT) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,622,059 | A→G | E97E (GAA→GAG) | yjjJ → | toxin YjjJ |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196273 | 1211435 | 15163 | 23 [22] | [20] 25 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 1428502–1428534 | 1428630 | 97–129 | 23 [22] | [20] 23 | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | * | ÷ | NC_000913 | 1632652–1632694 | 1633961–1633925 | 1232–1310 | 25 [22] | [22] 23 | ynfT–[pinQ] | ynfT,ydfK,[pinQ] |
| * | * | ÷ | NC_000913 | 3423776–3424234 | 3424527–3424239 | 6–752 | 24 [22] | [17] 23 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3762329–3764074 | 3765779–3765674 | 1601–3451 | 25 [22] | [21] 28 | rhsA | rhs element protein RhsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 112 (1.220) | 59/262 | 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 = | 153 (1.620) | 158 (1.680) | 70/268 | 0.1 | 66.1% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 10 (0.110) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 127 (1.340) | 69/270 | 0.1 | 96.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||