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 | 54,645 | C→T | A20T (GCT→ACT) | surA ← | peptidyl‑prolyl cis‑trans isomerase SurA |
| RA | 103,073 | A→G | S281G (AGC→GGC) | ddlB → | D‑alanine‑‑D‑alanine ligase B |
| RA | 107,553 | (T)9→8 | intergenic (+79/‑152) | lpxC → / → secM | UDP‑3‑O‑acyl‑N‑acetylglucosamine deacetylase/SecA translation regulator |
| RA | 177,839 | C→T | S208S (TCG→TCA) | btuF ← | vitamin B12 ABC transporter periplasmic binding protein |
| RA | 212,602 | C→T | A91V (GCC→GTC) | tilS → | tRNA(Ile)‑lysidine synthetase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 286,949 | Δ1 bp | coding (161/1611 nt) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| RA | 289,119 | T→G | D15A (GAC→GCC) | xynR ← | CP4‑6 prophage; DNA‑binding transcriptional repressor XynR |
| RA | 376,672 | G→A | intergenic (+2/‑100) | mhpT → / → yaiL | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter/DUF2058 domain‑containing protein YaiL |
| RA | 426,744 | T→C | V203A (GTA→GCA) | tgt → | tRNA‑guanine transglycosylase |
| RA | 440,973 | A→G | G43G (GGT→GGC) | ispA ← | geranyl diphosphate/farnesyl diphosphate synthase |
| RA | 460,213 | A→G | E442E (GAA→GAG) | lon → | Lon protease |
| RA | 468,365 | (A)7→6 | intergenic (+135/‑18) | cof → / → decR | HMP‑PP phosphatase/DNA‑binding transcriptional activator DecR |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 564,410 | (T)7→8 | coding (71/633 nt) | fimZ ← | putative LuxR family transcriptional regulator FimZ |
| RA | 604,738 | G→A | intergenic (‑75/+33) | ybdG ← / ← nfsB | miniconductance mechanosensitive channel YbdG/NAD(P)H nitroreductase NfsB |
| RA | 635,672 | G→A | P300S (CCA→TCA) | ybdN ← | putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 636,404 | (T)7→8 | coding (166/1221 nt) | ybdN ← | putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 643,316 | (G)6→7 | coding (1229/1239 nt) | ybdR → | putative Zn(2(+))‑dependent alcohol dehydrogenase YbdR |
| RA | 685,941 | (C)6→5 | coding (729/741 nt) | gltJ ← | glutamate/aspartate ABC transporter membrane subunit GltJ |
| RA | 732,698 | A→G | N1039S (AAC→AGC) | rhsC → | rhs element protein RhsC |
| RA | 784,695 | A→G | G43G (GGT→GGC) | zitB ← | Zn(2(+))/Cd(2(+))/Ni(2(+))/Cu(2(+)) exporter |
| RA | 787,153 | A→G | L148P (CTG→CCG) | gpmA ← | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| RA | 842,550 | C→T | D73D (GAC→GAT) | rlmF → | 23S rRNA m(6)A1618 methyltransferase |
| RA | 864,935 | C→T | T65T (ACG→ACA) | moeB ← | molybdopterin‑synthase adenylyltransferase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 896,954 | T→C | L274P (CTA→CCA) | potH → | putrescine ABC transporter membrane subunit PotH |
| RA | 911,302 | T→C | T283T (ACA→ACG) | hcr ← | NADH oxidoreductase |
| RA | 917,642 | Δ1 bp | coding (1170/1659 nt) | ybjD → | DUF2813 domain‑containing protein YbjD |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 966,280 | T→C | V654A (GTG→GCG) | ycaI → | conserved inner membrane protein YcaI |
| RA | 986,142 | A→G | L281L (TTA→CTA) | ompF ← | outer membrane porin F |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,018,976 | (A)8→7 | intergenic (+39/+37) | matP → / ← ompA | macrodomain Ter protein/outer membrane porin A |
| RA | 1,026,812 | (C)6→7 | coding (204/459 nt) | mgsA ← | methylglyoxal synthase |
| RA | 1,049,827 | T→G | intergenic (‑83/‑6) | gfcA ← / → insA‑4 | threonine‑rich inner membrane protein GfcA/IS1 protein InsA |
| RA | 1,059,570 | A→G | V105V (GTA→GTG) | torA → | trimethylamine N‑oxide reductase 1 |
| RA | 1,136,183 | A→G | Y207C (TAC→TGC) | flgH → | flagellar L‑ring protein |
| RA | 1,138,393 | A→G | N6D (AAT→GAT) | flgK → | flagellar hook‑filament junction protein 1 |
| RA | 1,142,777 | T→G | T531P (ACC→CCC) | rne ← | ribonuclease E |
| 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 | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,227,776 | (A)8→7 | coding (96/327 nt) | ycgL → | PF05166 family protein YcgL |
| RA | 1,294,216 | G→A | intergenic (+72/+210) | tdk → / ← insZ | thymidine/deoxyuridine kinase/putative transposase InsZ |
| RA | 1,318,251 | A→G | R55R (CGT→CGC) | trpB ← | tryptophan synthase subunit beta |
| RA | 1,361,250 | C→T | A44V (GCG→GTG) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,361,613 | (G)6→7 | coding (494/765 nt) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,416,377 | A→G | V337A (GTC→GCC) | recE ← | Rac prophage; exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific |
| RA | 1,421,638 | (C)7→8 | coding (520/858 nt) | ydaU → | Rac prophage; DUF1376 domain‑containing protein YdaU |
| RA | 1,479,687 | (G)6→5 | coding (550/1758 nt) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,492,842 | G→A | A125T (GCC→ACC) | trg → | methyl‑accepting chemotaxis protein Trg |
| RA | 1,498,836 | G→A | M62I (ATG→ATA) | ydcH → | protein YdcH |
| RA | 1,507,873 | A→G | T365A (ACC→GCC) | rlhA → | 23S rRNA 5‑hydroxycytidine C2501 synthase |
| RA | 1,513,877 | A→G | K16R (AAG→AGG) | ydcU → | putative ABC transporter membrane subunit YdcU |
| RA | 1,521,361 | T→C | T569A (ACC→GCC) | yncD ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,538,623 | A→G | R77R (CGT→CGC) | narY ← | nitrate reductase Z subunit beta |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,572,583 | C→T | V874I (GTT→ATT) | pqqL ← | putative zinc peptidase |
| RA | 1,591,717 | C→T | A154T (GCA→ACA) | hipA ← | serine/threonine kinase HipA |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,619,304 | (A)5→4 | coding (185/435 nt) | marR → | DNA‑binding transcriptional repressor MarR |
| RA | 1,629,137 | (A)6→7 | intergenic (+99/‑78) | ydfH → / → ydfZ | DNA‑binding transcriptional repressor YdfH/putative selenoprotein YdfZ |
| 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 | 1,873,384 | 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 | 1,939,463 | A→G | V244A (GTT→GCT) | lpxM ← | myristoyl‑acyl carrier protein‑dependent acyltransferase |
| RA | 1,945,042 | T→C | E105E (GAA→GAG) | ruvB ← | Holliday junction branch migration complex subunit RuvB |
| RA | 1,947,589 | G→A | A188V (GCG→GTG) | yebC ← | putative transcriptional regulator YebC |
| RA | 1,952,038 | T→C | V215A (GTC→GCC) | yecE → | DUF72 domain‑containing protein YecE |
| RA | 1,955,825 | Δ1 bp | coding (1183/2430 nt) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,988,106 | (C)6→5 | intergenic (‑147/‑116) | azuC ← / → yecR | uncharacterized protein AzuC/lipoprotein YecR |
| RA | 1,995,649 | (A)6→7 | intergenic (‑290/‑6) | uvrY ← / → yecU | DNA‑binding transcriptional activator UvrY/protein YecU |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 2,026,736 | G→A | H428Y (CAT→TAT) | dgcQ ← | putative diguanylate cyclase DgcQ |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,217,529 | G→A | F343F (TTC→TTT) | yehY ← | glycine betaine ABC transporter membrane subunit YehY |
| RA | 2,343,512 | G→A | P220S (CCT→TCT) | yfaL ← | putative autotransporter adhesin YfaL |
| RA | 2,345,057 | G→A | A65T (GCT→ACT) | nrdA → | ribonucleoside‑diphosphate reductase 1 subunit alpha |
| RA | 2,378,869 | T→C | T131A (ACG→GCG) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase |
| RA | 2,390,421 | T→C | Y362C (TAC→TGC) | nuoN ← | NADH:quinone oxidoreductase subunit N |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,472,006 | +C | pseudogene (57/519 nt) | yfdL ← | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,529,157 | A→T | V340V (GTT→GTA) | ligA ← | DNA ligase |
| RA | 2,678,019 | +G | coding (343/1512 nt) | yphE ← | putative ABC transporter ATP‑binding protein YphE |
| RA | 2,699,776 | T→C | C38C (TGT→TGC) | yfhL → | putative 4Fe‑4S cluster‑containing protein YfhL |
| RA | 2,773,137 | C→T | pseudogene (46/1016 nt) | yfjV ← | CP4‑57 prophage; putative arsenite transporter, N‑terminal fragment |
| 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 | 2,860,452 | T→C | intergenic (+36/+15) | pphB → / ← ygbI | phosphoprotein phosphatase 2/putative DeoR‑type DNA‑binding transcriptional regulator YgbI |
| RA | 2,867,926 | (C)6→5 | coding (828/1140 nt) | nlpD ← | murein hydrolase activator NlpD |
| RA | 2,895,838 | T→C | T240A (ACG→GCG) | ygcR ← | putative flavoprotein |
| RA | 2,905,388 | T→C | T11A (ACC→GCC) | queE ← | putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,994,202 | (A)7→8 | pseudogene (264/503 nt) | pbl → | transglycosylase domain‑containing protein Pbl |
| RA | 3,009,524 | T→C | V254A (GTA→GCA) | ygeY → | putative peptidase YgeY |
| RA | 3,015,088 | T→C | intergenic (‑31/‑72) | yqeC ← / → mocA | uncharacterized protein YqeC/molybdenum cofactor cytidylyltransferase |
| RA | 3,046,050 | T→C | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,092,566 | (G)6→5 | coding (689/951 nt) | gshB → | glutathione synthetase |
| RA | 3,099,063 | G→A | A168V (GCG→GTG) | yggM ← | DUF1202 domain‑containing protein YggM |
| RA | 3,117,047 | T→C | N689S (AAC→AGC) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,216,481 | (G)6→7 | coding (11/765 nt) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | 3,222,157 | G→A | R231Q (CGG→CAG) | ebgR → | DNA‑binding transcriptional repressor EbgR |
| JC | 3,240,984 | (G)7→10 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,338,135 | T→C | E109E (GAA→GAG) | mlaD ← | intermembrane phospholipid transport system, substrate binding protein MlaD |
| RA | 3,340,904 | G→A | T210T (ACG→ACA) | yrbG → | putative transport protein YrbG |
| 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 | 3,461,863 | C→T | I132I (ATC→ATT) | gspH → | Type II secretion system protein GspH |
| RA | 3,480,853 | Δ1 bp | coding (309/555 nt) | kefG ← | protein required for KefB activity |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,664,369 | G→A | Q84* (CAG→TAG) | gadW ← | DNA‑binding transcriptional dual regulator GadW |
| RA | 3,709,561 | (C)6→5 | coding (915/1692 nt) | eptB ← | Kdo2‑lipid A phosphoethanolamine 7''‑transferase |
| RA | 3,742,316 | T→C | T73A (ACC→GCC) | yiaJ ← | DNA‑binding transcriptional repressor YiaJ |
| RA | 3,749,448 | T→C | C73R (TGC→CGC) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,830,940 | A→G | T162A (ACG→GCG) | yicH → | AsmA famly protein YicH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,918,437 | T→C | Y474C (TAC→TGC) | atpA ← | ATP synthase F1 complex subunit alpha |
| RA | 3,931,183 | (G)7→8 | intergenic (‑90/‑133) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 3,953,304 | G→A | G274D (GGC→GAC) | ilvE → | branched‑chain‑amino‑acid aminotransferase |
| RA | 3,968,246 | A→G | M111V (ATG→GTG) | rfe → | UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase |
| RA | 3,974,520 | T→C | G18G (GGT→GGC) | rffC → | dTDP‑4‑amino‑4,6‑dideoxy‑D‑galactose acyltransferase |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 3,993,461 | A→G | H770R (CAC→CGC) | cyaA → | adenylate cyclase |
| RA | 4,023,933 | A→G | H127R (CAC→CGC) | tatD → | 3' ‑> 5' ssDNA/RNA exonuclease TatD |
| RA | 4,047,025 | C→T | R20R (CGC→CGT) | polA → | DNA polymerase I |
| RA | 4,055,093 | C→T | G62G (GGG→GGA) | glnG ← | DNA‑binding transcriptional dual regulator NtrC |
| RA | 4,057,622 | T→C | D138G (GAC→GGC) | glnA ← | glutamine synthetase |
| RA | 4,057,712 | A→G | I108T (ATT→ACT) | glnA ← | glutamine synthetase |
| RA | 4,116,996 | G→A | A76V (GCA→GTA) | glpK ← | glycerol kinase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,304,117 | T→C | intergenic (‑8/+11) | mdtN ← / ← ytcA | putative multidrug efflux pump membrane fusion protein/putative lipoprotein YtcA |
| RA | 4,330,676 | (G)5→6 | coding (175/1503 nt) | proP → | osmolyte:H(+) symporter ProP |
| RA | 4,330,680 | A→G | D60G (GAC→GGC) | proP → | osmolyte:H(+) symporter ProP |
| RA | 4,353,920 | A→G | G266G (GGT→GGC) | lysU ← | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| RA | 4,424,143 | C→T | I148I (ATC→ATT) | ulaF → | L‑ribulose‑5‑phosphate 4‑epimerase UlaF |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,472,004 | C→T | G131D (GGC→GAC) | pyrB ← | aspartate carbamoyltransferase catalytic subunit |
| RA | 4,484,372 | T→C | intergenic (‑92/+68) | holC ← / ← pepA | DNA polymerase III subunit chi/aminopeptidase A/I |
| JC | 4,488,579 | (C)7→10 | coding (1485/1503 nt) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,565,777 | A→G | V25A (GTC→GCC) | yjiM ← | putative dehydratase subunit |
| RA | 4,584,183 | A→G | V860A (GTG→GCG) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,592,406 | Δ1 bp | coding (750/1656 nt) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| 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 | 1049857–1050407 | 1050434–1050410 | 4–578 | 25 [22] | [23] 24 | [insA‑4]–[insB‑4] | [insA‑4],[insB‑4] |
| * | * | ÷ | NC_000913 | 1196245 | 1211438 | 15194 | 29 [21] | [23] 30 | [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 | 3423737–3424234 | 3424546–3424239 | 6–810 | 24 [23] | [23] 24 | [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) | 83 (1.030) | 51/268 | 0.3 | 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 = | 105 (1.270) | 91 (1.110) | 55/274 | 0.2 | 62.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 5 (0.060) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 92 (1.110) | 59/276 | 0.2 | 96.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||