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 |
| RA | 33,407 | T→G | 15.4% | V864G (GTG→GGG) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 55,437 | A→C | 10.6% | V558G (GTG→GGG) | lptD ← | LPS assembly OM complex LptDE, beta‑barrel component |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 328,024 | A→C | 14.5% | V237G (GTG→GGG) | betB ← | betaine aldehyde dehydrogenase, NAD‑dependent |
| RA | 337,463 | A→G | 20.9% | E229G (GAG→GGG) | yahF → | putative NAD(P)‑binding succinyl‑CoA synthase |
| RA | 433,649 | T→G | 20.3% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 29.4% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 599,581 | A→G | 16.1% | I290V (ATC→GTC) | cusA → | copper/silver efflux system, membrane component |
| RA | 811,721 | T→G | 30.5% | V67G (GTG→GGG) | bioC → | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| RA | 825,233 | C→A | 11.9% | M292I (ATG→ATT) | ybhR ← | putative ABC transporter permease |
| RA | 954,360 | T→A | 12.1% | Y36F (TAT→TTT) | focA ← | formate channel |
| RA | 954,374 | C→G | 10.0% | P31P (CCG→CCC) | focA ← | formate channel |
| RA | 1,126,894:1 | +G | 5.6% | coding (89/924 nt) | yceM → | putative oxidoreductase |
| RA | 1,196,131 | G→A | 31.2% | A337T (GCC→ACC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,305 | C→T | 49.6% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,287,149 | G→A | 6.5% | noncoding (88/171 nt) R10* (CGA→TGA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like 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 |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,466,201 | T→C | 5.4% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,432 | A→G | 8.5% | pseudogene (1041/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,438 | T→G | 6.0% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,579 | G→C | 9.6% | pseudogene (1188/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,708,844 | C→G | 12.3% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase 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 | 2,040,143 | A→G | 19.8% | V222V (GTA→GTG) | yedY → | membrane‑anchored, periplasmic TMAO, DMSO reductase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,151,689 | G→T | 31.5% | 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 | 2,228,229 | G→C | 17.0% | pseudogene (381/1287 nt) | mdtQ ← | pseudogene; putative channel/filament proteins |
| RA | 2,480,380 | A→G | 14.6% | G393G (GGA→GGG) | dsdA → | D‑serine dehydratase |
| RA | 2,509,880 | A→C | 17.8% | D84A (GAC→GCC) | yfeO → | putative ion channel protein |
| JC JC | 2,536,312 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | 7.8% | coding (479‑484/510 nt) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 3,053,585 | T→G | 9.6% | N419T (AAC→ACC) | pepP ← | proline aminopeptidase P II |
| RA | 3,206,438 | G→A | 18.4% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,467 | T→G | 8.5% | M2R (ATG→AGG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,471 | C→G | 13.3% | S3R (AGC→AGG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,477 | T→A | 19.3% | S5R (AGT→AGA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,483 | G→A | 22.7% | K7K (AAG→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,484 | C→A | 13.4% | Q8K (CAA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,494 | T→G | 12.1% | V11G (GTG→GGG) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,495 | G→A | 13.6% | V11V (GTG→GTA) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,506 | C→A | 12.3% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,520,796 | G→T | 10.7% | 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 | 3,560,494 | G→A | 8.8% | pseudogene (112/150 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,714,371 | G→T | 8.2% | A675D (GCC→GAC) | bisC ← | biotin sulfoxide reductase |
| RA | 3,760,369 | T→C | 16.8% | D294G (GAC→GGC) | selA ← | selenocysteine synthase |
| RA | 3,786,542 | T→G | 10.7% | V428G (GTC→GGC) | gpmM → | phosphoglycero mutase III, cofactor‑independent |
| RA | 3,813,072 | A→C | 19.5% | T114T (ACA→ACC) | dfp → | fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding |
| RA | 3,815,500 | T→G | 11.3% | D90A (GAC→GCC) | pyrE ← | orotate phosphoribosyltransferase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,821,099 | G→A | 5.3% | A24A (GCC→GCT) | ligB ← | DNA ligase, NAD(+)‑dependent |
| RA | 3,862,661 | T→G | 30.8% | pseudogene (943/1617 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 | 3,862,662 | T→G | 21.2% | pseudogene (942/1617 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 | 3,862,670 | T→A | 18.1% | 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 | 3,872,495 | T→G | 5.6% | A168A (GCA→GCC) | dgoD ← | D‑galactonate dehydratase |
| RA | 3,971,097 | T→G | 15.2% | V322G (GTG→GGG) | wecB → | UDP‑N‑acetyl glucosamine‑2‑epimerase |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,027,132 | A→G | 13.8% | G202G (GGA→GGG) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,144,660 | T→C | 7.4% | R222R (CGT→CGC) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,145,076 | A→C | 14.4% | N361T (AAC→ACC) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| JC JC | 4,160,853 | IS2 (+) +5 bp | 8.0% | intergenic (‑63/‑267) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,219,539 | C→T | 10.4% | A315V (GCG→GTG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,274,843 | T→G | 8.4% | T67P (ACC→CCC) | yjcB ← | putative inner membrane protein |
| RA | 4,296,060 | C→T | 9.8% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 12.5% | 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 | 4,307,559 | T→G | 13.2% | T81P (ACC→CCC) | alsK ← | D‑allose kinase |
| RA | 4,421,183 | A→C | 15.7% | T402P (ACC→CCC) | ulaA → | L‑ascorbate‑specific enzyme IIC permease component of PTS |
| RA | 4,465,778 | T→C | 10.2% | I135V (ATC→GTC) | treB ← | trehalose‑specific PTS enzyme: IIB and IIC component |
| RA | 4,590,879 | T→C | 11.4% | D134G (GAC→GGC) | yjiY ← | putative transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2033744 | 2034051 | 308 | 41 [36] | [36] 48 | [yedS] | [yedS] |
| * | * | ÷ | NC_000913 | 3423852–3424451 | 3424451 | 1–600 | 41 [40] | [40] 45 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233763 | 4235411 | 1649 | 41 [39] | [40] 42 | [pgi] | [pgi] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 458792 = | 106 (0.840) | 18 (0.140) | 14/420 | NT | 14.5% | intergenic (+92/‑96) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608007 = | NA (NA) | noncoding (1/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 33 (0.260) | 120 (1.010) | 75/396 | NT | 82.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 21 (0.180) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 33 (0.260) | 92 (0.780) | 64/396 | NT | 78.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 21 (0.180) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 39 (0.320) | 31/412 | 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 | |||||