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 | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 353,610 | C→G | 13.0% | A302G (GCG→GGG) | prpE → | propionate‑‑CoA ligase |
| RA | 385,818 | T→G | 13.9% | V196G (GTC→GGC) | tauA → | taurine ABC transporter periplasmic binding protein |
| RA | 422,231 | A→T | 13.8% | I416F (ATC→TTC) | proY → | proline‑specific permease |
| RA | 433,649 | T→G | 26.2% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,792 | IS186 (–) +4 bp | 100% | intergenic (+92/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 599,612 | T→G | 14.3% | V300G (GTG→GGG) | cusA → | copper/silver efflux system, membrane component |
| RA | 630,187 | A→G | 13.0% | G98G (GGA→GGG) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 825,230 | C→A | 15.1% | M293I (ATG→ATT) | ybhR ← | putative ABC transporter permease |
| RA | 836,592 | T→G | 16.1% | V81G (GTC→GGC) | ybiC → | putative dehydrogenase |
| RA | 836,625 | T→G | 13.6% | V92G (GTC→GGC) | ybiC → | putative dehydrogenase |
| RA | 954,374 | C→G | 13.5% | P31P (CCG→CCC) | focA ← | formate channel |
| RA | 989,943 | T→G | 22.9% | S138S (TCA→TCC) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 989,959 | A→C | 18.8% | V133G (GTA→GGA) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,143,829 | A→C | 94.5% | L180R (CTG→CGG) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,258,972 | C→G | 7.6% | A61G (GCC→GGC) | ychH → | DUF2583 family putative inner membrane protein |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,358,812 | A→G | 20.1% | S126P (TCC→CCC) | puuP ← | putrescine importer |
| RA | 1,611,919 | C→A | 16.7% | intergenic (‑65/+47) | yneF ← / ← yneG | putative membrane‑bound diguanylate cyclase/DUF4186 family protein |
| RA | 1,706,082 | T→G | 8.5% | F106V (TTT→GTT) | rsxA → | SoxR iron‑sulfur cluster reduction factor component; inner membrane protein of electron transport complex |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,043,020 | Δ1 bp | 8.3% | intergenic (+122/+448) | yodB → / ← serU | cytochrome b561 homolog/tRNA‑Ser |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,151,689 | G→T | 26.7% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,304,522 | G→T | 6.1% | intergenic (+129/+586) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,523 | G→C | 6.0% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,378,969 | T→C | 15.9% | G97G (GGA→GGG) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| RA | 2,383,623 | A→T | 25.0% | D304V (GAT→GTT) | elaD → | protease, capable of cleaving an AMC‑ubiquitin model substrate |
| RA | 2,434,882 | T→G | 22.9% | Y252S (TAC→TCC) | truA ← | tRNA pseudouridine(38‑40) synthase |
| RA | 2,608,231 | A→G | 14.7% | M439V (ATG→GTG) | hyfF → | hydrogenase 4, membrane subunit |
| RA | 2,828,506 | T→G | 20.8% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 2,833,567 | T→G | 17.5% | G364G (GGT→GGG) | norV → | anaerobic nitric oxide reductase flavorubredoxin |
| RA | 3,206,438 | G→A | 18.1% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,456 | A→G | 10.0% | intergenic (‑200/‑7) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,458 | T→G | 10.4% | intergenic (‑202/‑5) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,469 | A→G | 9.3% | S3G (AGC→GGC) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,471 | C→G | 18.1% | S3R (AGC→AGG) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,476 | G→A | 10.0% | S5N (AGT→AAT) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,477 | T→A | 18.8% | S5R (AGT→AGA) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,483 | G→A | 30.1% | K7K (AAG→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,484 | C→A | 16.3% | Q8K (CAA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,487 | C→A | 18.4% | Q9K (CAG→AAG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,520,796 | G→T | 8.5% | T75K (ACA→AAA) | hofP ← | DNA catabolic protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,760,384 | A→C | 17.4% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| RA | 3,782,908 | T→G | 25.5% | T252P (ACC→CCC) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| RA | 3,782,913 | A→C | 17.1% | V250G (GTG→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,862,670 | T→A | 29.6% | pseudogene (934/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,864,959 | T→C | 18.6% | I439V (ATC→GTC) | yidE ← | putative transporter |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,027,146 | C→G | 16.0% | A207G (GCG→GGG) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,151,329 | T→G | 31.2% | A590A (GCA→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,237,261 | T→C | 20.2% | V122A (GTC→GCC) | yjbG → | extracellular polysaccharide export OMA protein |
| RA | 4,296,060 | C→T | 18.5% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 11.8% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,325,948 | A→G | 5.1% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,394,322 | T→G | 12.8% | V86G (GTC→GGC) | nnr → | bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 384786 | 385076 | 291 | 40 [38] | [36] 40 | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 583140 | 583824 | 685 | 43 [36] | [39] 41 | [appY] | [appY] |
| * | * | ÷ | NC_000913 | 1978500 | 1979280 | 781 | 42 [39] | [39] 41 | insB1–insA | insB1,insA |
| * | * | ÷ | NC_000913 | 3423865–3424233 | 3424455–3424239 | 7–591 | 40 [39] | [38] 42 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3798877 | 3799533 | 657 | 40 [39] | [39] 40 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 4233737 | 4235454 | 1718 | 41 [38] | [38] 44 | pgi | pgi |
| * | * | ÷ | NC_000913 | 4476738 | 4477169 | 432 | 40 [38] | [38] 42 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 366099 | 90 (0.800) | 5 (0.050) | 5/410 | NT | 5.3% | coding (207/3075 nt) | lacZ | beta‑D‑galactosidase |
| ? | NC_000913 | = 366105 | 93 (0.870) | coding (201/3075 nt) | lacZ | beta‑D‑galactosidase | |||||
| * | ? | NC_000913 | 1207790 = | 92 (0.810) | 26 (0.250) | 23/400 | NT | 26.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 61 (0.580) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 90 (0.800) | 25 (0.240) | 21/400 | NT | 25.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 61 (0.580) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 34 (0.310) | 32/424 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 34 (0.310) | 25/416 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 4542682 = | 15 (0.130) | 6 (0.060) | 6/414 | NT | 13.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 61 (0.560) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||