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 | 28,122 | A→G | K277R (AAG→AGG) | rihC → | ribonucleoside hydrolase RihC |
| RA | 36,533 | A→G | V431A (GTC→GCC) | caiC ← | carnitine‑CoA ligase |
| RA | 103,093 | A→G | A287A (GCA→GCG) | ddlB → | D‑alanine‑‑D‑alanine ligase B |
| RA | 126,180 | G→A | V162V (GTG→GTA) | aceF → | pyruvate dehydrogenase, E2 subunit |
| RA | 148,703 | A→G | G31G (GGT→GGC) | panC ← | pantothenate synthetase |
| RA | 162,902 | C→T | R266R (CGC→CGT) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
| RA | 164,603 | A→G | intergenic (+69/‑127) | hrpB → / → mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| RA | 187,877 | C→G | E258D (GAG→GAC) | glnD ← | PII uridylyltransferase/uridylyl removing enzyme |
| RA | 230,054 | A→G | R276R (CGT→CGC) | yafC ← | putative LysR family transcriptional regulator YafC |
| JC JC | 238,217 | IS1 (+) +9 bp | intergenic (+97/+32) | yafT → / ← ykfM | lipoprotein YafT/uncharacterized protein YkfM |
| RA | 251,015 | (G)6→7 | coding (118/1056 nt) | dinB → | DNA polymerase IV |
| RA | 267,354 | A→G | W218R (TGG→CGG) | yafZ ← | CP4‑6 prophage; conserved protein YafZ |
| RA | 273,690 | T→C | Y282H (TAT→CAT) | ykfC → | CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 298,837 | C→T | A700T (GCG→ACG) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 332,172 | T→C | intergenic (+296/‑199) | yahV → / → pdeL | protein YahV/DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| RA | 338,243 | A→G | D489G (GAT→GGT) | yahF → | putative acyl‑CoA synthetase YahF |
| RA | 338,763 | C→T | P147S (CCG→TCG) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 373,073 | C→T | G51G (GGC→GGT) | mhpF → | acetaldehyde dehydrogenase (acylating) |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 461,311 | (T)7→8 | intergenic (+69/‑140) | lon → / → hupB | Lon protease/DNA‑binding protein HU‑beta |
| RA | 484,432 | C→T | K396K (AAG→AAA) | acrA ← | multidrug efflux pump membrane fusion lipoprotein AcrA |
| RA | 507,338 | A→G | V248A (GTC→GCC) | ybaP ← | TraB family protein YbaP |
| RA | 547,455 | T→C | V259A (GTT→GCT) | fdrA → | putative acyl‑CoA synthetase FdrA |
| RA | 553,102 | C→T | intergenic (‑2/+116) | purE ← / ← lpxH | N(5)‑carboxyaminoimidazole ribonucleotide mutase/UDP‑2,3‑diacylglucosamine diphosphatase |
| RA | 583,763 | (A)8→7 | coding (83/750 nt) | appY → | DNA‑binding transcriptional activator AppY |
| RA | 597,290 | (A)7→8 | coding (160/333 nt) | cusF → | copper/silver export system periplasmic binding protein |
| RA | 746,213 | A→G | K93K (AAA→AAG) | nei → | endonuclease VIII |
| RA | 837,167 | A→G | T273A (ACC→GCC) | hcxB → | hydroxycarboxylate dehydrogenase B |
| RA | 868,422 | (C)8→10 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 967,268 | A→G | E216E (GAA→GAG) | msbA → | ATP‑binding lipopolysaccharide transport protein |
| RA | 1,004,160 | (G)7→8 | coding (214/711 nt) | ycbF → | putative fimbrial chaperone YcbF |
| RA | 1,047,492 | G→A | P152S (CCA→TCA) | gfcD ← | putative lipoprotein GfcD |
| RA | 1,074,507 | C→T | A89V (GCC→GTC) | rutR → | DNA‑binding transcriptional dual regulator RutR |
| RA | 1,089,047 | A→G | F271L (TTC→CTC) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase |
| RA | 1,134,888 | (G)5→4 | coding (160/783 nt) | flgG → | flagellar basal‑body rod protein FlgG |
| RA | 1,158,924 | C→T | S352S (AGC→AGT) | ptsG → | glucose‑specific PTS enzyme IIBC component |
| RA | 1,168,194 | (T)7→6 | intergenic (+56/+6) | ycfJ → / ← comR | PF05433 family protein YcfJ/DNA‑binding transcriptional repressor ComR |
| RA | 1,217,796 | Δ1 bp | coding (469/1524 nt) | pdeG → | putative c‑di‑GMP phosphodiesterase PdeG |
| RA | 1,231,534 | A→G | T117A (ACT→GCT) | umuC → | DNA polymerase V catalytic protein |
| RA | 1,296,104 | C→T | G673D (GGT→GAT) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,298,712 | A→G | T39A (ACA→GCA) | ychE → | putative inner membrane protein |
| RA | 1,339,842 | A→G | A171A (GCA→GCG) | pgpB → | phosphatidylglycerophosphatase B |
| RA | 1,340,487 | A→G | E82G (GAA→GGA) | lapA → | lipopolysaccharide assembly protein A |
| RA | 1,354,337 | T→C | Y61C (TAT→TGT) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,368,978 | C→A | L60M (CTG→ATG) | pspB → | phage shock protein B |
| RA | 1,394,008 | A→G | D261G (GAT→GGT) | mppA → | murein tripeptide ABC transporter periplasmic binding protein |
| RA | 1,408,229 | G→A | P60P (CCG→CCA) | zntB → | Zn(2(+)):H(+) symporter |
| RA | 1,409,269 | T→C | intergenic (+22/‑39) | fnrS → / → ynaL | small regulatory RNA FnrS/protein YnaL |
| RA | 1,574,588 | G→A | A205A (GCC→GCT) | pqqL ← | putative zinc peptidase |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,606,004 | T→C | G318G (GGT→GGC) | lsrB → | Autoinducer‑2 ABC transporter periplasmic binding protein |
| RA | 1,621,918 | T→C | V196A (GTC→GCC) | ydeE → | dipeptide exporter |
| RA | 1,624,874 | C→A | R34R (CGC→CGA) | ydeJ → | conserved protein YdeJ |
| RA | 1,632,316 | T→C | intergenic (‑31/‑574) | ydfJ ← / → ynfT | putative transporter YdfJ/Qin prophage; protein YnfT |
| RA | 1,691,255 | T→C | G468G (GGT→GGC) | ydgA → | conserved protein YdgA |
| RA | 1,699,674 | T→C | V107A (GTA→GCA) | malX → | PTS enzyme IIBC component MalX |
| RA | 1,728,113 | G→A | G93R (GGG→AGG) | gloA → | glyoxalase I |
| RA | 1,797,160 | T→C | Q262R (CAG→CGG) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| RA | 1,797,414 | A→G | R177R (CGT→CGC) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| RA | 1,828,320 | T→C | D472G (GAC→GGC) | astD ← | aldehyde dehydrogenase |
| JC JC | 1,873,031 | IS1 (–) +9 bp | coding (991‑999/1491 nt) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,883,393 | G→A | R69H (CGT→CAT) | yeaV → | putative transporter YeaV |
| RA | 1,916,745 | T→C | V163A (GTA→GCA) | yebS → | intermembrane transport protein YebS |
| RA | 1,917,424 | A→G | G389G (GGA→GGG) | yebS → | intermembrane transport protein YebS |
| RA | 1,922,480 | T→C | S164G (AGC→GGC) | pphA ← | phosphoprotein phosphatase 1 |
| RA | 1,965,567 | (A)5→4 | coding (625/1149 nt) | flhB ← | flagellar biosynthesis protein FlhB |
| RA | 2,010,681 | C→T | Q28* (CAG→TAG) | yedL → | putative acetyltransferase YedL |
| RA | 2,013,366 | (C)5→6 | coding (138/1659 nt) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,018,530 | (C)6→7 | coding (145/1128 nt) | fliK → | flagellar hook‑length control protein |
| RA | 2,021,565 | T→C | V21A (GTG→GCG) | fliO → | flagellar biosynthesis protein FliO |
| RA | 2,039,162 | A→G | G69G (GGA→GGG) | yedX → | hydroxyisourate hydrolase/transthyretin‑related protein |
| RA | 2,202,336 | A→G | K686K (AAA→AAG) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,272,287 | T→C | intergenic (+5/‑77) | pdeN → / → yejA | putative c‑di‑GMP phosphodiesterase PdeN/putative oligopeptide ABC transporter periplasmic binding protein |
| RA | 2,299,097 | T→C | N161S (AAC→AGC) | napH ← | ferredoxin‑type protein NapH |
| RA | 2,351,657 | T→C | T240A (ACG→GCG) | glpT ← | sn‑glycerol 3‑phosphate:phosphate antiporter |
| RA | 2,364,849 | T→C | V99A (GTT→GCT) | nudI → | pyrimidine deoxynucleotide diphosphatase NudI |
| RA | 2,381,278 | (T)5→6 | coding (266/462 nt) | elaA ← | putative N‑acetyltransferase ElaA |
| RA | 2,433,807 | T→C | E40E (GAA→GAG) | accD ← | acetyl‑CoA carboxyltransferase subunit beta |
| RA | 2,462,003 | G→A | G233D (GGC→GAC) | fadL → | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor |
| 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 | 2,465,498 | G→A | A66A (GCG→GCA) | yfdC → | inner membrane protein YfdC |
| RA | 2,545,264 | T→C | T116A (ACC→GCC) | murR ← | DNA‑binding transcriptional dual regulator MurR |
| RA | 2,610,430 | C→T | A89A (GCC→GCT) | hyfH → | hydrogenase 4 component H |
| RA | 2,725,612 | T→C | S45S (TCA→TCG) | kgtP ← | alpha‑ketoglutarate:H(+) symporter |
| RA | 2,747,735 | G→A | R21C (CGC→TGC) | ffh ← | signal recognition particle protein component |
| RA | 2,793,973 | T→C | G413G (GGT→GGC) | gabT → | 4‑aminobutyrate aminotransferase GabT |
| RA | 2,797,325 | A→G | T39A (ACC→GCC) | ygaV → | putative DNA‑binding transcriptional regulator YgaV |
| RA | 2,812,669 | G→A | A18A (GCG→GCA) | emrB → | multidrug efflux pump membrane subunit EmrB |
| RA | 2,821,424 | G→C | G196G (GGC→GGG) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 2,935,939 | T→C | V119A (GTT→GCT) | fucI → | L‑fucose isomerase |
| RA | 2,958,239 | G→A | Q216* (CAG→TAG) | ptrA ← | protease 3 |
| RA | 2,987,611 | T→C | S26P (TCA→CCA) | yqeH → | putative LuxR family transcriptional regulator YqeH |
| RA | 3,012,391 | T→C | *311Q (TAA→CAA) | yqeA → | putative amino acid kinase YqeA |
| RA | 3,039,049 | A→G | V232A (GTG→GCG) | xerD ← | site‑specific recombinase |
| RA | 3,045,845 | T→C | L19L (TTA→TTG) | ygfF ← | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 3,053,229 | T→C | Y97C (TAC→TGC) | ubiH ← | 2‑octaprenyl‑6‑methoxyphenol hydroxylase |
| RA | 3,079,836 | T→C | V600V (GTA→GTG) | tktA ← | transketolase 1 |
| RA | 3,089,159 | (G)5→4 | coding (876/1395 nt) | galP → | galactose:H(+) symporter |
| RA | 3,113,979 | (C)5→4 | coding (374/810 nt) | pppA ← | prepilin peptidase |
| RA | 3,197,348 | A→G | V765A (GTG→GCG) | glnE ← | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
| RA | 3,201,469 | A→G | E88G (GAG→GGG) | ygiM → | putative signal transduction protein (SH3 domain) |
| RA | 3,258,242 | (A)8→7 | intergenic (‑232/+43) | cyuP ← / ← tdcG | putative D/L‑serine transporter/L‑serine deaminase III |
| RA | 3,304,813 | (C)7→6 | coding (1005/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,327,860 | T→C | L24P (CTT→CCT) | yhbY → | ribosome assembly factor YhbY |
| RA | 3,349,443 | T→C | T123A (ACA→GCA) | mtgA ← | peptidoglycan glycosyltransferase MtgA |
| RA | 3,355,164 | G→A | G147D (GGC→GAC) | gltB → | glutamate synthase subunit GltB |
| RA | 3,383,303 | T→C | intergenic (+36/+27) | degS → / ← mdh | serine endoprotease/malate dehydrogenase |
| RA | 3,389,557 | T→C | V13A (GTA→GCA) | aaeR → | LysR‑type transcriptional regulator AaeR |
| RA | 3,487,116 | G→A | G109E (GGG→GAG) | yhfK → | putative transporter YhfK |
| RA | 3,584,362 | A→G | intergenic (+53/‑42) | yrhA → / → yrhD | putative uncharacterized protein YrhA/uncharacterized protein YrhD |
| RA | 3,644,774 | A→G | F137L (TTT→CTT) | prlC ← | oligopeptidase A |
| RA | 3,646,061 | T→C | V226A (GTA→GCA) | rlmJ → | 23S rRNA m(6)A2030 methyltransferase |
| RA | 3,728,118 | (C)8→9 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | 3,751,654 | (T)7→6 | coding (215/741 nt) | yiaT ← | outer membrane protein YiaT |
| RA | 3,786,454 | T→C | Y399H (TAT→CAT) | gpmM → | 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | 3,866,015 | G→A | R87C (CGC→TGC) | yidE ← | putative transport protein YidE |
| RA | 3,877,994 | C→T | R709H (CGT→CAT) | gyrB ← | DNA gyrase subunit B |
| RA | 3,901,422 | T→C | K267E (AAA→GAA) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,955,324 | (G)6→7 | coding (1847/1851 nt) | ilvD → | dihydroxy‑acid dehydratase |
| RA | 3,964,010 | T→C | I74V (ATT→GTT) | gpp ← | guanosine‑5'‑triphosphate,3'‑diphosphate phosphatase |
| RA | 4,105,642 | T→C | D10G (GAC→GGC) | cpxR ← | DNA‑binding transcriptional dual regulator CpxR |
| RA | 4,266,319 | A→G | T180A (ACC→GCC) | alr → | alanine racemase 1 |
| RA | 4,296,380 | 1 bp→GCG | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,298,407 | A→G | G320G (GGT→GGC) | fdhF ← | formate dehydrogenase H |
| RA | 4,327,379 | A→G | K82R (AAA→AGA) | crfC → | clamp‑binding sister replication fork colocalization protein |
| RA | 4,359,906 | A→G | G42G (GGT→GGC) | cadB ← | lysine:cadaverine antiporter |
| RA | 4,373,758 | T→C | S159S (TCA→TCG) | yjeJ ← | protein YjeJ |
| RA | 4,398,650 | G→A | A413A (GCG→GCA) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,458,870 | G→A | T304T (ACG→ACA) | pmbA → | metalloprotease PmbA |
| RA | 4,532,965 | C→T | A73A (GCG→GCA) | yjhP ← | KpLE2 phage‑like element; putative methyltransferase YjhP |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 361202 | 361914 | 713 | 197 [192] | [191] 196 | lacA | lacA |
| * | * | ÷ | NC_000913 | 2856995 | 2857095 | 101 | 198 [192] | [0] 345 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423690–3424234 | 3424608–3424238 | 5–919 | 197 [193] | [194] 196 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 70046 = | 328 (0.980) | 335 (1.040) | 151/188 | 0.2 | 67.8% | coding (3/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 2857096 = | 0 (0.000) | coding (4/2562 nt) | mutS | DNA mismatch repair protein MutS | |||||