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 | 249,318 | C→A | pseudogene (753/1713 nt) | lfhA ← | flagellar system protein, promoterless fragment |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 299,481 | C→A | G485V (GGC→GTC) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 321,694 | C→A | L29L (CTC→CTA) | ykgE → | putative lactate utilization oxidoreductase YkgE |
| RA | 357,088 | C→A | G306G (GGC→GGA) | codA → | cytosine/isoguanine deaminase |
| RA | 409,944 | G→T | Q26K (CAG→AAG) | rdgC ← | nucleoid‑associated protein RdgC |
| RA | 718,191 | G→T | S25S (TCC→TCA) | potE ← | putrescine:H(+) symporter/putrescine:ornithine antiporter PotE |
| RA | 743,216 | G→T | W130C (TGG→TGT) | ybgI → | radiation resistance protein YbgI |
| RA | 793,635 | C→A | E52* (GAA→TAA) | modF ← | ABC family protein ModF |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 904,732 | C→A | S47Y (TCC→TAC) | ybjQ → | putative heavy metal binding protein YbjQ |
| RA | 989,846 | G→T | L171M (CTG→ATG) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,046,028 | C→A | G640C (GGC→TGC) | gfcD ← | putative lipoprotein GfcD |
| 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 | 1,264,184 | T→C | D157D (GAT→GAC) | hemA → | glutamyl‑tRNA reductase |
| RA | 1,275,139 | C→A | F452L (TTC→TTA) | ychO → | putative invasin YchO |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,311,838 | C→A | intergenic (+30/+10) | tonB → / ← yciA | Ton complex subunit TonB/acyl‑CoA thioesterase |
| RA | 1,334,817 | G→T | L321L (CTG→CTT) | cysB → | DNA‑binding transcriptional dual regulator CysB |
| RA | 1,368,075 | C→G | intergenic (‑163/‑4) | pspF ← / → pspA | DNA‑binding transcriptional dual regulator PspF/phage shock protein A |
| RA | 1,404,352 | G→T | Q72K (CAA→AAA) | abgA ← | p‑aminobenzoyl‑glutamate hydrolase subunit A |
| RA | 1,425,640 | A→C | *88Y (TAA→TAC) N7T (AAC→ACC) |
ynaK → ydaY → |
Rac prophage; ParB‑like nuclease domain‑containing protein YnaK Rac prophage; putative uncharacterized protein YdaY |
| RA | 1,482,407 | G→C | L152V (CTG→GTG) | azoR ← | FMN dependent NADH:quinone oxidoreductase |
| RA | 1,556,899 | G→C | G92A (GGT→GCT) | osmC → | osmotically inducible peroxiredoxin |
| RA | 1,602,751 | C→A | S421* (TCG→TAG) | lsrA → | Autoinducer‑2 ABC transporter ATP binding subunit |
| RA | 1,616,161 | G→T | K133N (AAG→AAT) | yneK → | protein YneK |
| RA | 1,621,227 | G→T | intergenic (‑90/‑105) | eamA ← / → ydeE | cysteine/O‑acetylserine exporter EamA/dipeptide exporter |
| RA | 1,648,021 | C→A | L30M (CTG→ATG) | dicA → | DNA‑binding transcriptional dual regulator DicA |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,752,236 | G→C | T532R (ACG→AGG) | ydhV ← | putative oxidoreductase |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,923,004 | C→A | intergenic (‑35/‑62) | pphA ← / → ryeA | phosphoprotein phosphatase 1/small RNA RyeA |
| RA | 1,929,733 | G→T | intergenic (‑26/+301) | yebE ← / ← yebF | conserved inner membrane protein YebE/secreted protein YebF |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,002,780 | G→T | A276D (GCT→GAT) | fliC ← | flagellar filament structural protein |
| RA | 2,008,206 | C→A | intergenic (‑116/‑71) | yedD ← / → yedE | lipoprotein YedD/putative selenium transporter YedE |
| RA | 2,087,341 | T→C | K306K (AAA→AAG) | yeeY ← | putative DNA‑binding transcriptional regulator YeeY |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,269,808 | C→A | intergenic (+241/‑171) | lpxT → / → mepS | Kdo2‑lipid A phosphotransferase/peptidoglycan DD‑endopeptidase/peptidoglycan LD‑carboxypeptidase |
| RA | 2,333,979 | G→T | pseudogene (424/4605 nt) | yfaS ← | putative macroglobulin family protein, N‑terminal fragment |
| RA | 2,376,054 | G→T | L256M (CTG→ATG) | menB ← | 1,4‑dihydroxy‑2‑naphthoyl‑CoA synthase |
| RA | 2,508,176 | G→T | Q23K (CAG→AAG) | fryB ← | putative PTS enzyme IIB component FryB |
| RA | 2,510,966 | G→T | intergenic (+80/‑35) | yfeO → / → ypeC | putative transport protein YfeO/DUF2502 domain‑containing protein YpeC |
| RA | 2,585,759 | G→T | S10I (AGT→ATT) | narQ → | sensory histidine kinase NarQ |
| RA | 2,588,261 | C→G | P223A (CCT→GCT) | acrD → | multidrug efflux pump RND permease AcrD |
| RA | 2,621,836 | G→T | D214Y (GAT→TAT) | purM → | phosphoribosylformylglycinamide cyclo‑ligase |
| RA | 2,764,025 | G→T | L377I (CTT→ATT) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| RA | 2,773,416 | (T)8→7 | coding (99/1704 nt) | yfjW → | CP4‑57 prophage; uncharacterized protein YfjW |
| RA | 2,901,468 | A→C | I293L (ATC→CTC) | yqcE → | putative transport protein YqcE |
| RA | 2,954,431 | G→T | Q525K (CAA→AAA) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 3,009,263 | C→A | P167Q (CCG→CAG) | ygeY → | putative peptidase YgeY |
| RA | 3,042,847 | G→T | P101Q (CCG→CAG) | yqfA ← | hemolysin‑III family protein |
| RA | 3,057,844 | G→T | G189G (GGC→GGA) | serA ← | phosphoglycerate dehydrogenase |
| RA | 3,154,419 | G→T | A267E (GCG→GAG) | yqhC ← | DNA‑binding transcriptional activator YqhC |
| RA | 3,185,014 | C→A | L59M (CTG→ATG) | ubiK → | ubiquinone biosynthesis accessory factor UbiK |
| RA | 3,215,442 | C→A | R11L (CGG→CTG) | mug ← | stationary phase mismatch/uracil DNA glycosylase |
| RA | 3,238,922 | C→A | L115M (CTG→ATG) | alx → | putative membrane‑bound redox modulator Alx |
| RA | 3,261,774 | G→T | G215G (GGC→GGA) | tdcE ← | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,377,264 | G→T | L53I (CTC→ATC) | sspA ← | stringent starvation protein A |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,585,618 | G→T | N402K (AAC→AAA) | ggt ← | glutathione hydrolase proenzyme |
| RA | 3,614,131 | G→T | L155L (CTG→CTT) | nikA → | Ni(2(+)) ABC transporter periplasmic binding protein |
| RA | 3,616,203 | C→A | R8S (CGC→AGC) | nikC → | Ni(2(+)) ABC transporter membrane subunit NikC |
| RA | 3,796,064 | C→A | P29Q (CCA→CAA) | waaC → | ADP‑heptose:LPS heptosyltransferase 1 |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,815,942 | G→T | T203K (ACG→AAG) | rph ← | truncated RNase PH |
| RA | 3,818,801 | C→A | intergenic (+217/‑73) | dinD → / → yicG | DNA damage‑inducible protein D/conserved inner membrane protein YicG |
| RA | 3,844,637 | C→A | A225D (GCC→GAC) | adeD → | adenine deaminase |
| RA | 4,041,319 | C→A | G39W (GGG→TGG) | mobB ← | molybdopterin‑guanine dinucleotide biosynthesis adaptor protein |
| RA | 4,128,053 | C→A | intergenic (‑159/+25) | yiiX ← / ← metJ | putative lipid binding hydrolase/DNA‑binding transcriptional repressor MetJ |
| RA | 4,146,727 | C→A | A157E (GCA→GAA) | pflC → | putative pyruvate formate‑lyase 2 activating enzyme PflC |
| RA | 4,224,754 | C→A | G309G (GGC→GGA) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,479,084 | C→A | G152C (GGC→TGC) | yjgM ← | putative acetyltransferase YjgM |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196286 | 1211428 | 15143 | 12 [10] | [11] 15 | [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 | 3102988 | 3104051 | 1064 | 13 [11] | [9] 13 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423770–3424231 | 3424545–3424239 | 9–776 | 12 [11] | [11] 12 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3762358–3764074 | 3765191–3764077 | 4–2834 | 12 [11] | [11] 12 | rhsA | rhs element protein RhsA |
| * | * | ÷ | NC_000913 | 3943694–3943987 | 3945482–3944061 | 75–1789 | 12 [10] | [11] 12 | [rrlC] | [rrlC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 17 (0.490) | 6/192 | 2.8 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 28 (0.590) | 14/262 | 1.9 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 7 (0.200) | 6/192 | 2.8 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 3363001 = | 81 (1.600) | 70 (1.390) | 49/276 | 0.0 | 63.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 46 (0.910) | 34/278 | 0.3 | 97.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||