mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 249,587 | T→G | 13.6% | pseudogene (484/1713 nt) | lfhA ← | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,168 | G→A | 5.1% | intergenic (+287/‑291) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,176 | A→G | 9.1% | intergenic (+295/‑283) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 433,649 | T→G | 16.5% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 31.9% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 628,868 | T→G | 25.4% | G106G (GGT→GGG) | entA → | 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase |
| RA | 630,187 | A→G | 12.9% | G98G (GGA→GGG) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 647,210 | A→C | 17.8% | G100G (GGT→GGG) | citG ← | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase |
| RA | 729,695 | T→G | 23.4% | V38G (GTG→GGG) | rhsC → | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 811,721 | T→G | 16.5% | V67G (GTG→GGG) | bioC → | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| RA | 989,901 | G→T | 17.8% | S152R (AGC→AGA) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 989,943 | T→G | 21.5% | S138S (TCA→TCC) ‡ | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 989,945 | A→G | 19.6% | S138P (TCA→CCA) ‡ | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,196,131 | G→A | 17.9% | A337T (GCC→ACC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,305 | C→T | 31.9% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,258,996 | T→G | 19.1% | V69G (GTG→GGG) | ychH → | DUF2583 family putative inner membrane protein |
| RA | 1,286,974 | C→T | 8.8% | intergenic (+448/+92) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| 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 | 1,478,418 | G→T | 11.2% | A65S (GCG→TCG) | ynbB → | putative CDP‑diglyceride synthase |
| RA | 1,708,805 | T→C | 16.5% | R629R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,890,491 | A→C | 16.1% | G14G (GGT→GGG) | yeaY ← | Slp family lipoprotein, RpoE‑regulated |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,151,689 | G→T | 38.6% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| RA | 2,159,421 | A→T | 15.9% | I346F (ATT→TTT) | mdtC → | multidrug efflux system, subunit C |
| 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 | 2,185,199 | T→G | 19.1% | T35P (ACC→CCC) | thiM ← | hydoxyethylthiazole kinase |
| RA | 2,283,059 | C→A | 26.5% | D297Y (GAT→TAT) | yejK ← | spermidine nucleoid‑associated protein |
| RA | 2,304,798 | T→C | 18.8% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,367,368 | G→T | 17.7% | D100Y (GAT→TAT) | arnC → | undecaprenyl phosphate‑L‑Ara4FN transferase |
| JC JC | 2,536,312 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | 27.2% | coding (479‑484/510 nt) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,828,506 | T→G | 15.6% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 3,206,438 | G→A | 18.1% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,469 | A→G | 12.7% | S3G (AGC→GGC) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,471 | C→G | 8.4% | S3R (AGC→AGG) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,477 | T→A | 20.9% | S5R (AGT→AGA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,483 | G→A | 20.7% | K7K (AAG→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,484 | C→A | 10.9% | Q8K (CAA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,487 | C→A | 15.7% | Q9K (CAG→AAG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,506 | C→A | 10.8% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,370,875 | A→C | 12.1% | G54G (GGT→GGG) | nanE ← | putative N‑acetylmannosamine‑6‑P epimerase |
| RA | 3,492,834 | T→G | 18.1% | G89G (GGT→GGG) | tsgA → | putative transporter |
| RA | 3,551,917 | A→C | 10.5% | V186G (GTG→GGG) | malP ← | maltodextrin phosphorylase |
| 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 | 5.3% | pseudogene (112/150 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,568,771 | G→T | 13.0% | N186K (AAC→AAA) | glgC ← | glucose‑1‑phosphate adenylyltransferase |
| RA | 3,697,740 | T→G | 13.3% | V428G (GTG→GGG) | bcsE → | cellulose production protein |
| RA | 3,760,384 | A→C | 26.7% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| RA | 3,765,271 | A→G | 10.3% | D1030G (GAC→GGC) | rhsA → | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,780,896 | T→G | 11.1% | V357G (GTG→GGG) | lldD → | L‑lactate dehydrogenase, FMN‑linked |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,852,516 | T→G | 18.7% | N90T (AAC→ACC) | ilvB ← | acetolactate synthase 2 large subunit |
| RA | 3,862,616 | T→A | 13.8% | pseudogene (988/1617 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 | 3,862,658 | A→G | 18.6% | pseudogene (946/1617 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 | 3,862,661 | T→G | 43.7% | 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 | 3,862,670 | T→C | 18.6% | 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 | 3,862,673 | G→A | 16.1% | pseudogene (931/1617 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 | 3,862,686 | T→C | 14.8% | pseudogene (918/1617 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 | 3,927,435 | C→T | 5.0% | T94M (ACG→ATG) | asnA → | asparagine synthetase A |
| RA | 3,927,437 | C→T | 5.1% | H95Y (CAC→TAC) ‡ | asnA → | asparagine synthetase A |
| RA | 3,927,438 | A→G | 5.1% | H95R (CAC→CGC) ‡ | asnA → | asparagine synthetase A |
| RA | 3,927,440 | A→G | 5.1% | M96V (ATG→GTG) | asnA → | asparagine synthetase A |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,151,329 | T→G | 19.3% | A590A (GCA→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,160,854 | C→T | 10.6% | intergenic (‑64/‑270) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,162,526 | G→T | 5.2% | Q249K (CAA→AAA) | trmA ← | tRNA m(5)U54 methyltransferase, SAM‑dependent; tmRNA m(5)U341 methyltransferase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,209,827 | T→G | 17.2% | noncoding (54/76 nt) | gltV → | tRNA‑Glu |
| RA | 4,219,539 | C→T | 6.9% | A315V (GCG→GTG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,296,060 | C→T | 16.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 13.7% | 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 | 4,421,183 | A→C | 25.2% | T402P (ACC→CCC) | ulaA → | L‑ascorbate‑specific enzyme IIC permease component of PTS |
| RA | 4,555,119 | A→G | 10.7% | I182V (ATC→GTC) | uxuR → | fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1211933 | 1212782 | 850 | 42 [40] | [38] 41 | [iraM]–[ycgX] | [iraM],[ycgX] |
| * | * | ÷ | NC_000913 | 1299348 | 1300773 | 1426 | 41 [40] | [40] 41 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 2470052 | 2470715 | 664 | 41 [38] | [40] 42 | [gtrS] | [gtrS] |
| * | * | ÷ | NC_000913 | 3769543 | 3770191 | 649 | 41 [32] | [38] 42 | [yibV]–yibU | [yibV],yibV,yibU,yibU |
| * | * | ÷ | NC_000913 | 4233729 | 4235859 | 2131 | 41 [39] | [40] 41 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 12 (0.110) | 106 (1.020) | 65/406 | NT | 90.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 10 (0.100) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 13 (0.120) | 88 (0.850) | 59/406 | NT | 88.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 10 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 20 (0.180) | 19/430 | 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) | 35 (0.320) | 30/422 | 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 | 3927418 = | 113 (1.010) | 14 (0.130) | 12/414 | NT | 11.5% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 109 (1.030) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||