mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 58,464 | G→A | intergenic (+285/‑10) | djlA → / → yabP | co‑chaperone protein DjlA/putative uncharacterized protein YabP |
| RA | 123,994 | C→T | F326F (TTC→TTT) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 193,097 | C→A | P76T (CCG→ACG) | frr → | ribosome‑recycling factor |
| RA | 234,059 | C→A | A242S (GCA→TCA) | gloB ← | hydroxyacylglutathione hydrolase GloB |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 364,549 | C→T | W586* (TGG→TAG) | lacZ ← | beta‑galactosidase |
| RA | 402,781 | T→A | G345G (GGT→GGA) | phoA → | alkaline phosphatase |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 544,112 | G→T | A394D (GCC→GAC) | allC ← | allantoate amidohydrolase |
| RA | 545,199 | A→G | Y32H (TAT→CAT) | allC ← | allantoate amidohydrolase |
| RA | 637,977 | C→T | M199I (ATG→ATA) | dsbG ← | protein sulfenic acid reductase and chaperone DsbG |
| RA | 638,349 | C→T | E75E (GAG→GAA) | dsbG ← | protein sulfenic acid reductase and chaperone DsbG |
| RA | 658,938 | A→T | intergenic (‑1000/‑9) | crcB ← / → tatE | F(‑) channel protein/twin arginine protein translocation system ‑ TatE protein |
| RA | 690,948 | G→A | V279V (GTC→GTT) | ybeX ← | CorC‑HlyC family protein YbeX |
| RA | 700,038 | G→A | H97Y (CAT→TAT) | umpH ← | UMP phosphatase |
| MC JC | 725,040 | Δ4,101 bp | [kdpB]–[ybfA] | [kdpB], kdpA, kdpF, [ybfA] | |
| RA | 789,591 | G→A | S130F (TCC→TTC) | galK ← | galactokinase |
| RA | 809,217 | 2 bp→AG | coding (40‑41/1290 nt) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 827,122 | C→T | G44D (GGT→GAT) | ybhS ← | ABC exporter membrane subunit YbhS |
| RA | 884,185 | G→A | E171E (GAG→GAA) | mdfA → | multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 884,187 | G→T | G172V (GGG→GTG) | mdfA → | multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| JC JC | 891,856 | +AC :: IS30 (–) | coding (673/723 nt) | nfsA → | NADPH‑dependent nitro/quinone reductase NfsA |
| RA | 968,837 | G→A | D158N (GAT→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 1,040,126 | G→T | L277L (CTG→CTT) | appB → | cytochrome bd‑II subunit 2 |
| RA | 1,061,935 | G→A | S46N (AGC→AAC) | torD → | trimethylamine‑N‑oxide reductase‑specific chaperone |
| RA | 1,111,727 | 2 bp→TT | coding (865‑866/2544 nt) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| 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 | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,310,770 | A→G | H32H (CAT→CAC) | yciI ← | protein YciI |
| RA | 1,314,901 | G→T | I108I (ATC→ATA) | yciE ← | DUF892 domain‑containing protein YciE |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,357,202 | C→T | intergenic (‑92/+221) | sapA ← / ← ymjA | putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,365,327 | C→T | H366Y (CAC→TAC) | puuB → | gamma‑glutamylputrescine oxidase |
| RA | 1,408,945 | G→T | W299L (TGG→TTG) | zntB → | Zn(2(+)):H(+) symporter |
| RA | 1,462,805 | G→A | E227E (GAG→GAA) | paaK → | phenylacetate‑CoA ligase |
| RA | 1,531,689 | A→G | intergenic (‑1185/‑127) | yncO ← / → ydcC | protein YncO/H repeat‑associated putative transposase YdcC |
| RA | 1,553,630 | C→A | G70V (GGT→GTT) | adhP ← | ethanol dehydrogenase/alcohol dehydrogenase |
| RA | 1,555,731 | Δ1 bp | intergenic (‑62/+95) | maeA ← / ← sra | malate dehydrogenase (oxaloacetate‑decarboxylating)/ribosome‑associated protein Sra |
| RA | 1,562,884 | C→T | V65M (GTG→ATG) | ddpX ← | D‑alanyl‑D‑alanine dipeptidase |
| MC JC | 1,589,920 | Δ647 bp | [ydeT] | [ydeT] | |
| RA | 1,600,234 | C→T | intergenic (‑25/+54) | lsrK ← / ← lsrR | autoinducer‑2 kinase/DNA‑binding transcriptional repressor LsrR |
| RA | 1,601,098 | C→A | S48S (TCG→TCT) | lsrR ← | DNA‑binding transcriptional repressor LsrR |
| RA | 1,601,103 | C→T | V47M (GTG→ATG) | lsrR ← | DNA‑binding transcriptional repressor LsrR |
| RA | 1,632,712 | A→G | intergenic (‑427/‑178) | ydfJ ← / → ynfT | putative transporter YdfJ/protein YnfT |
| RA | 1,641,002 | T→C | intergenic (+27/+337) | ynfU → / ← cspB | putative zinc‑binding protein YnfU/cold shock‑like protein CspB |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,649,971 | C→T | P60S (CCG→TCG) | ydfD → | lysis protein |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,702,757 | C→T | F175F (TTC→TTT) | add → | adenosine deaminase |
| JC JC | 1,743,922 | IS2 (+) +5 bp | coding (466‑470/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,793,377 | Δ1 bp | coding (182/750 nt) | btuD ← | vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,819,586 | C→T | G74S (GGC→AGC) | chbA ← | N,N'‑diacetylchitobiose‑specific PTS enzyme IIA component |
| RA | 1,874,202 | G→A | intergenic (‑20/‑150) | yoaI ← / → yeaL | protein YoaI/DUF441 domain‑containing inner membrane protein YeaL |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,901,623 | G→A | L37L (CTG→TTG) | yoaL ← | protein YoaL |
| JC JC | 1,909,411 | IS2 (+) +5 bp | coding (685‑689/792 nt) | kdgR ← | DNA‑binding transcriptional repressor KdgR |
| RA | 1,911,929 | 2 bp→TT | coding (647‑648/882 nt) | htpX ← | protease HtpX |
| RA | 1,977,383 | G→T | S154R (AGC→AGA) | flhC ← | DNA‑binding transcriptional dual regulator FlhC |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,099,525 | A→T | I30N (ATT→AAT) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| RA | 2,111,259 | Δ1 bp | coding (718/900 nt) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,155,880 | C→T | L206L (CTC→CTT) | mdtB → | multidrug efflux pump RND permease subunit MdtB |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,173,448 | C→T | intergenic (‑575/+834) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,174,611 | IS5 (+) +4 bp | coding (436‑439/453 nt) | gatA ← | galactitol‑specific PTS enzyme IIA component |
| RA | 2,224,169 | A→G | F234F (TTT→TTC) | pbpG ← | peptidoglycan DD‑endopeptidase PbpG |
| RA | 2,237,105 | G→T | P217T (CCG→ACG) | mglC ← | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| JC JC | 2,237,684 | IS5 (+) +4 bp | coding (67‑70/1011 nt) | mglC ← | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| RA | 2,264,460 | 2 bp→AT | coding (598‑599/1182 nt) | setB → | sugar exporter SetB |
| RA | 2,319,078 | C→A | D267Y (GAT→TAT) | rcsC ← | histidine kinase RcsC |
| RA | 2,360,550 | Δ1 bp | coding (865/1206 nt) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,392,233 | C→G | G270A (GGT→GCT) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,470,649 | A→C | intergenic (‑6/+428) | yodE ← / ← yfdK | toxic protein YodE/putative tail fiber assembly protein YfdK |
| RA | 2,578,822 | G→A | D53N (GAT→AAT) | talA → | transaldolase A |
| RA | 2,654,802 | C→T | E44E (GAG→GAA) | sseB ← | protein SseB |
| RA | 2,725,532 | C→T | G72E (GGA→GAA) | kgtP ← | alpha‑ketoglutarate:H(+) symporter |
| JC JC | 2,913,392 | IS2 (–) +5 bp | coding (256‑260/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,942,741 | G→A | noncoding (46/206 nt) | gcvB → | small regulatory RNA GcvB |
| RA | 3,155,038 | G→C | R61G (CGT→GGT) | yqhC ← | DNA‑binding transcriptional activator YqhC |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,436,605 | G→A | D30N (GAT→AAT) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,437,885 | C→T | F456F (TTC→TTT) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,548,392 | T→C | D560G (GAT→GGT) | malQ ← | 4‑alpha‑glucanotransferase |
| RA | 3,553,419 | T→G | L112R (CTT→CGT) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,558,195 | G→T | intergenic (‑116/‑73) | rtcB ← / → rtcR | RNA‑splicing ligase/DNA‑binding transcriptional activator RtcR |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,665,945 | G→A | intergenic (‑135/+235) | gadX ← / ← gadA | DNA‑binding transcriptional dual regulator GadX/glutamate decarboxylase A |
| RA | 3,682,515 | C→T | M311I (ATG→ATA) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,769,447 | G→A | E35K (GAA→AAA) | yibV → | PF15596 family protein YibV |
| RA | 3,773,040 | (G)6→4 | coding (760‑761/1914 nt) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,783,983 | G→A | S49F (TCC→TTC) | secB ← | protein export chaperone SecB |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,819,501 | C→T | G557D (GGT→GAT) | ligB ← | DNA ligase B |
| RA | 3,865,885 | A→G | V130A (GTT→GCT) | yidE ← | putative transport protein YidE |
| RA | 3,899,195 | C→T | E67K (GAA→AAA) | yieK ← | putative glucosamine‑6‑phosphate deaminase YieK |
| RA | 3,903,234 | G→A | V156V (GTC→GTT) | bglB ← | 6‑phospho‑beta‑glucosidase B |
| RA | 3,932,137 | Δ1 bp | coding (822/1869 nt) | kup → | K(+):H(+) symporter Kup |
| RA | 3,932,491 | G→A | W392* (TGG→TGA) | kup → | K(+):H(+) symporter Kup |
| RA | 3,961,662 | G→T | G329V (GGC→GTC) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 3,965,174 | G→A | H153Y (CAC→TAC) | rhlB ← | ATP‑dependent RNA helicase RhlB |
| RA | 3,968,683 | G→A | M256I (ATG→ATA) | rfe → | UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase |
| RA | 3,969,748 | T→C | S240P (TCG→CCG) | wzzE → | enterobacterial common antigen polysaccharide co‑polymerase |
| RA | 3,993,531 | T→C | R793R (CGT→CGC) | cyaA → | adenylate cyclase |
| RA | 4,009,698 | G→A | A177T (GCA→ACA) | pldB → | lysophospholipase L2 |
| RA | 4,017,197 | C→T | intergenic (+5/‑136) | udp → / → rmuC | uridine phosphorylase/putative recombination limiting protein RmuC |
| RA | 4,077,859 | G→A | G137G (GGG→GGA) | fabY → | putative fatty acid biosynthesis enzyme FabY |
| RA | 4,084,287 | G→A | F512F (TTC→TTT) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,113,851 | G→A | H208Y (CAT→TAT) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,193,996 | T→G | D70A (GAT→GCT) | thiE ← | thiamine phosphate synthase |
| RA | 4,215,347 | T→A | intergenic (+138/‑131) | metA → / → aceB | homoserine O‑succinyltransferase/malate synthase A |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,293,781 | 2 bp→AT | coding (239‑240/597 nt) | nrfG → | putative formate‑dependent nitrite reductase complex subunit NrfG |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,400,254 | C→T | intergenic (+52/‑34) | miaA → / → hfq | tRNA dimethylallyltransferase/RNA‑binding protein Hfq |
| RA | 4,473,900 | C→T | G52R (GGA→AGA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,475,493 | T→C | F19F (TTT→TTC) | yjgL → | protein YjgL |
| RA | 4,504,996 | C→T | L313L (CTC→CTT) | nanX → | sialic acid transporter NanX |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,546,601 | C→T | I502I (ATC→ATT) | fimD → | type I fimbriae usher protein |
| JC JC | 4,572,868 | +GA :: IS3 (+) +4 bp | coding (455‑458/1518 nt) | yjiT → | putative uncharacterized protein YjiT |
| RA | 4,611,733 | 2 bp→TT | coding (338‑339/606 nt) | osmY → | periplasmic chaperone OsmY |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 226500–226603 | 228498–226988 | 386–1999 | 33 [32] | [32] 33 | rrlH | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 1196304 | 1211460 | 15157 | 33 [32] | [28] 33 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1632734–1632847 | 1633402–1633224 | 378–669 | 33 [31] | [32] 33 | ynfT–ydfK | ynfT,ydfK |
| * | * | ÷ | NC_000913 | 3423812–3424230 | 3424457–3424239 | 10–646 | 34 [32] | [32] 33 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 315229 = | NA (NA) | 100 (1.080) +T |
64/596 | 0.2 | 88.5% | noncoding (1/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 2169995 | 13 (0.140) | pseudogene (173/475 nt) | gatR | DNA‑binding transcriptional repressor GatR, N‑terminal fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 141 (1.530) | 88/590 | 0.0 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1652250 = | 45 (0.480) | 74 (0.790) | 53/598 | 0.6 | 62.2% | intergenic (+2265/+478) | ydfD/ynfP | lysis protein/protein YnfP |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1652253 | 45 (0.480) | 61 (0.650) | 49/598 | 0.7 | 57.6% | intergenic (+2268/+475) | ydfD/ynfP | lysis protein/protein YnfP |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2102943 | NA (NA) | 81 (0.870) | 57/596 | 0.4 | 77.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2110236 = | 23 (0.250) | coding (784/882 nt) | rfbA | glucose‑1‑phosphate thymidylyltransferase 1 | |||||