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 | 101,492 | T→C | V243A (GTG→GCG) | murC → | UDP‑N‑acetylmuramate‑‑L‑alanine ligase |
| RA | 184,266 | T→C | E268E (GAA→GAG) | yaeI ← | phosphodiesterase YaeI |
| RA | 197,199 | T→C | R218R (CGT→CGC) | rseP → | intramembrane zinc metalloprotease |
| RA | 209,567 | A→G | Y316C (TAC→TGC) | accA → | acetyl‑CoA carboxyltransferase subunit alpha |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 283,866 | C→T | G222G (GGC→GGT) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 373,802 | T→C | T294T (ACT→ACC) | mhpF → | acetaldehyde dehydrogenase (acylating) |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 396,911 | T→C | T91T (ACT→ACC) | sbmA → | peptide antibiotic/peptide nucleic acid transporter |
| RA | 508,296 | A→G | I27V (ATC→GTC) | ybaQ → | putative DNA‑binding transcriptional regulator YbaQ |
| RA | 518,551 | A→G | V200A (GTC→GCC) | ybbO ← | NADP(+)‑dependent aldehyde reductase |
| RA | 524,426 | A→G | D389G (GAC→GGC) | rhsD → | protein RhsD |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 625,143 | T→C | S87P (TCG→CCG) | entC → | isochorismate synthase EntC |
| RA | 727,838 | T→C | M299V (ATG→GTG) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 744,382 | A→C | D47A (GAC→GCC) | pxpC → | 5‑oxoprolinase component C |
| RA | 748,647 | T→C | G112G (GGA→GGG) | ybgO ← | putative fimbrial protein YbgO |
| RA | 854,321 | A→G | G225G (GGA→GGG) | ybiR → | putative transporter YbiR |
| RA | 868,422 | (C)8→9 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 869,831 | A→G | T141A (ACA→GCA) | gsiB → | glutathione ABC transporter periplasmic binding protein |
| 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 | 934,909 | G→A | T562T (ACG→ACA) | ftsK → | cell division DNA translocase FtsK |
| RA | 959,905 | A→G | Y365C (TAC→TGC) | aroA → | 3‑phosphoshikimate 1‑carboxyvinyltransferase |
| RA | 1,002,743 | A→G | T313A (ACA→GCA) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,003,901 | G→A | V155M (GTG→ATG) | ycbV → | putative fimbrial protein YcbV |
| RA | 1,004,160 | (G)7→8 | coding (214/711 nt) | ycbF → | putative fimbrial chaperone YcbF |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,057,911 | T→C | Q15R (CAG→CGG) | torR ← | DNA‑binding transcriptional dual regulator TorR |
| RA | 1,066,950 | C→T | D48N (GAT→AAT) | yccJ ← | PF13993 family protein YccJ |
| RA | 1,099,997 | C→T | L120L (CTG→TTG) | ycdY → | chaperone protein YcdY |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,144,444 | C→T | intergenic (‑77/‑58) | rne ← / → yceQ | ribonuclease E/DUF2655 domain‑containing protein YceQ |
| RA | 1,187,155 | C→T | A362A (GCG→GCA) | roxA ← | ribosomal protein‑arginine oxygenase |
| RA | 1,204,239 | G→A | pseudogene (70/234 nt) A24T (GCA→ACA) |
oweE → ymfN → |
phage replication protein e14 prophage; chimeric replication protein/phage terminase YmfN |
| RA | 1,212,088 | (C)8→7 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,227,874 | A→G | N65S (AAT→AGT) | ycgL → | PF05166 family protein YcgL |
| RA | 1,292,420 | (T)7→6 | intergenic (+55/+89) | galU → / ← hns | UTP‑‑glucose‑1‑phosphate uridylyltransferase/DNA‑binding transcriptional dual regulator H‑NS |
| RA | 1,311,576 | A→G | Y163C (TAT→TGT) | tonB → | Ton complex subunit TonB |
| RA | 1,321,941 | C→T | A336T (GCC→ACC) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,389,344 | A→G | T139A (ACA→GCA) | ycjG → | L‑Ala‑D/L‑Glu epimerase |
| RA | 1,477,305 | T→C | V721A (GTA→GCA) | ydbD → | DUF2773 domain‑containing protein YdbD |
| RA | 1,488,705 | C→T | L158L (CTC→CTT) | aldA → | aldehyde dehydrogenase A |
| RA | 1,515,011 | A→G | T84A (ACG→GCG) | ydcV → | putative ABC transporter membrane subunit YdcV |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,586,168 | C→T | G107R (GGG→AGG) | ydeP ← | putative oxidoreductase YdeP |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,614,810 | C→T | L3L (CTG→TTG) | yneJ → | putative LysR‑type DNA‑binding transcriptional regulator YneJ |
| RA | 1,635,023 | T→C | A275A (GCA→GCG) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,026 | A→G | H274H (CAT→CAC) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,029 | C→T | A273A (GCG→GCA) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,032 | G→A | G272G (GGC→GGT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,654,330 | T→C | D271G (GAC→GGC) | rspA ← | mandelate racemase/muconate lactonizing enzyme family protein RspA |
| RA | 1,673,215 | A→C | V96G (GTC→GGC) | mdtJ ← | multidrug/spermidine efflux pump membrane subunit MdtJ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,736,263 | G→A | A343V (GCT→GTT) | ydhP ← | putative transporter YdhP |
| RA | 1,753,426 | G→A | A135A (GCC→GCT) | ydhV ← | putative oxidoreductase |
| RA | 1,772,189 | T→C | A373A (GCT→GCC) | ydiM → | putative exporter YdiM |
| RA | 1,780,622 | G→A | L74L (CTG→CTA) | ydiR → | putative electron transfer flavoprotein subunit YdiR |
| RA | 1,790,537 | G→A | V236V (GTC→GTT) | ydiU ← | UPF0061 family protein YdiU |
| RA | 1,790,861 | T→C | I128M (ATA→ATG) | ydiU ← | UPF0061 family protein YdiU |
| RA | 1,797,151 | T→C | H265R (CAC→CGC) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| 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 | 1,892,710 | A→G | Y176H (TAT→CAT) | yoaA ← | putative 5' to 3' DNA helicase implicated in DNA repair |
| RA | 1,924,089 | A→G | V168A (GTG→GCG) | yebZ ← | putative inner membrane protein |
| RA | 1,928,311 | Δ1 bp | coding (529/2061 nt) | ptrB ← | oligopeptidase B |
| RA | 1,942,675 | T→C | V5A (GTT→GCT) | znuC → | Zn(2(+)) ABC transporter ATP binding subunit |
| RA | 1,977,215 | (A)8→9 | intergenic (‑76/+51) | motA ← / ← flhC | motility protein A/DNA‑binding transcriptional dual regulator FlhC |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,992,659 | T→C | A53A (GCA→GCG) | pgsA ← | phosphatidylglycerophosphate synthase |
| RA | 2,012,809 | T→C | N69S (AAC→AGC) | fliE ← | flagellar basal‑body protein FliE |
| RA | 2,052,846 | T→C | pseudogene (483/1053 nt) | yeeL ← | putative glycosyltransferase, N‑terminal fragment |
| RA | 2,088,033 | T→C | T76A (ACC→GCC) | yeeY ← | putative DNA‑binding transcriptional regulator YeeY |
| RA | 2,105,102 | A→G | V319A (GTT→GCT) | wbbI ← | beta‑1,6‑galactofuranosyltransferase |
| RA | 2,114,034 | G→A | T98T (ACC→ACT) | galF ← | UTP:glucose‑1‑phosphate uridylyltransferase, low activity |
| RA | 2,134,956 | T→C | T233A (ACT→GCT) | wzc ← | protein‑tyrosine kinase Wzc |
| RA | 2,147,379 | T→C | I54M (ATA→ATG) | alkA ← | DNA‑3‑methyladenine glycosylase 2 |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,226,089 | A→G | I97V (ATT→GTT) | yohD → | DedA family protein YohD |
| RA | 2,227,170 | T→C | H34R (CAC→CGC) | yohF ← | putative oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 2,267,414 | Δ1 bp | coding (1170/1467 nt) | yeiQ → | putative dehydrogenase, NAD‑dependent |
| RA | 2,297,856 | T→C | E135G (GAG→GGG) | napC ← | periplasmic nitrate reductase cytochrome c protein |
| RA | 2,340,934 | G→A | A1079V (GCC→GTC) | yfaL ← | putative autotransporter adhesin YfaL |
| RA | 2,355,854 | G→A | V112I (GTC→ATC) | glpC → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit C |
| RA | 2,370,617 | G→A | W200* (TGG→TGA) | arnD → | putative 4‑deoxy‑4‑formamido‑L‑arabinose‑phosphoundecaprenol deformylase ArnD |
| RA | 2,438,793 | C→T | R282W (CGG→TGG) | flk → | putative flagella assembly protein |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,448,685 | A→G | Q27R (CAG→CGG) | smrB → | putative endonuclease SmrB |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,540,599 | A→G | R72R (CGT→CGC) | cysA ← | sulfate/thiosulfate ABC transporter ATP binding subunit |
| RA | 2,544,253 | A→G | V124A (GTG→GCG) | ucpA ← | putative oxidoreductase |
| RA | 2,567,131 | T→C | N326S (AAC→AGC) | eutH ← | putative inner membrane protein |
| RA | 2,612,257 | T→C | F120L (TTT→CTT) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,650,173 | T→C | K705K (AAA→AAG) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,661,656 | T→C | K159R (AAG→AGG) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,662,890 | A→G | L145P (CTG→CCG) | trmJ ← | tRNA Cm32/Um32 methyltransferase |
| RA | 2,736,296 | G→A | A51T (GCA→ACA) | bamD → | outer membrane protein assembly factor BamD |
| RA | 2,746,406 | T→C | intergenic (‑221/+28) | rpsP ← / ← ffh | 30S ribosomal subunit protein S16/signal recognition particle protein component |
| RA | 2,765,204 | T→C | intergenic (‑51/+309) | abpA ← / ← yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| RA | 2,769,444 | G→A | A260A (GCG→GCA) | yfjQ → | CP4‑57 prophage; protein YfjQ |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,819,957 | T→C | E685E (GAA→GAG) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,873,008 | T→C | intergenic (‑188/+6) | ftsB ← / ← ygbE | cell division protein FtsB/conserved inner membrane protein YgbE |
| RA | 2,907,474 | A→G | G156G (GGT→GGC) | eno ← | enolase |
| RA | 2,911,637 | A→G | V672A (GTA→GCA) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,926,961 | G→A | S218S (TCG→TCA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,950,194 | A→G | Q318R (CAG→CGG) | argA → | N‑acetylglutamate synthase |
| RA | 2,972,315 | C→T | T240M (ACG→ATG) | tas → | putative NADP(H)‑dependent aldo‑keto reductase Tas |
| RA | 3,027,944 | T→C | V275A (GTG→GCG) | ghxQ → | guanine/hypoxanthine transporter GhxQ |
| RA | 3,053,565 | (T)5→4 | coding (1276/1326 nt) | pepP ← | proline aminopeptidase P II |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,102,340 | (C)6→5 | coding (513/720 nt) | trmI ← | tRNA m(7)G46 methyltransferase |
| RA | 3,116,287 | G→A | S942S (AGC→AGT) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,191,392 | T→C | V254A (GTC→GCC) | yqiI → | putative fimbrial protein YqiI |
| RA | 3,218,087 | A→G | G330G (GGT→GGC) | aer ← | aerotaxis sensor receptor, flavoprotein |
| RA | 3,237,681 | C→T | A124V (GCC→GTC) | ygjR → | putative oxidoreductase YgjR |
| RA | 3,245,633 | G→A | G137D (GGC→GAC) | exuT → | hexuronate transporter |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,357,504 | T→C | V927A (GTC→GCC) | gltB → | glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,537,286 | T→C | *159Q (TAA→CAA) | greB → | transcription elongation factor GreB |
| RA | 3,538,312 | G→A | V310I (GTC→ATC) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,555,613 | A→G | V843V (GTA→GTG) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,702,492 | A→G | L126P (CTG→CCG) | dppF ← | dipeptide ABC transporter ATP binding subunit DppF |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,819,380 | C→T | N169N (AAC→AAT) | yicG → | conserved inner membrane protein YicG |
| RA | 3,826,614 | A→G | T469A (ACC→GCC) | recG → | ATP‑dependent DNA helicase RecG |
| RA | 3,840,260 | C→T | P16S (CCA→TCA) | yicS → | uncharacterized protein YicS |
| RA | 3,846,404 | A→G | V255A (GTG→GCG) | 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 | 3,941,273 | C→T | A19T (GCT→ACT) | yieP ← | putative transcriptional regulator YieP |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,003,939 | G→A | A80A (GCC→GCT) | rarD ← | putative transporter RarD |
| RA | 4,097,247 | A→G | C68R (TGC→CGC) | rhaB ← | rhamnulokinase |
| RA | 4,183,301 | A→G | Q686R (CAA→CGA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,206,545 | T→G | T330P (ACC→CCC) | purH ← | bifunctional AICAR transformylase/IMP cyclohydrolase |
| RA | 4,222,887 | T→C | T248A (ACC→GCC) | iclR ← | DNA‑binding transcriptional repressor IclR |
| RA | 4,295,851 | 2 bp→AA | intergenic (+57/+584) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,578 | T→C | Y183C (TAC→TGC) | yjcO ← | Sel1 repeat‑containing protein YjcO |
| RA | 4,326,835 | A→G | intergenic (‑101/‑300) | yjdM ← / → crfC | conserved protein YjdM/clamp‑binding sister replication fork colocalization protein |
| RA | 4,434,695 | C→T | G624E (GGG→GAG) | cpdB ← | 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,468,660 | G→A | V346I (GTA→ATA) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | 4,515,997 | C→T | V227V (GTG→GTA) | fecA ← | ferric citrate outer membrane transporter |
| RA | 4,537,490 | A→G | D35D (GAT→GAC) | nanS ← | N‑acetyl‑9‑O‑acetylneuraminate esterase |
| RA | 4,634,239 | T→C | V148A (GTG→GCG) | ytjC → | putative phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1633313–1633625 | 1634966–1634640 | 1016–1654 | 15 [14] | [11] 16 | pinQ–[ydfN] | pinQ,tfaQ,[ydfN] |
| * | * | ÷ | NC_000913 | 3423755–3424234 | 3424545–3424239 | 6–791 | 16 [14] | [14] 15 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4295902 | 4296343 | 442 | 15 [14] | [14] 16 | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 70 (1.200) | 51/266 | 0.1 | 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 = | 86 (1.440) | 99 (1.660) | 62/272 | 0.0 | 69.1% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 67 (1.120) | 43/274 | 0.3 | 95.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||