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 | 12,484 | C→A | 17.9% | Q108K (CAG→AAG) | dnaK → | chaperone Hsp70, with co‑chaperone DnaJ |
| RA | 114,216 | A→G | 9.0% | E258G (GAG→GGG) | guaC → | GMP reductase |
| RA | 249,538 | T→G | 12.4% | pseudogene (533/1713 nt) | lfhA ← | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 284,003 | A→G | 21.5% | E268G (GAG→GGG) | yagF → | CP4‑6 prophage; dehydratase family protein |
| RA | 388,233 | A→G | 13.8% | S147G (AGT→GGT) | tauD → | taurine dioxygenase, 2‑oxoglutarate‑dependent |
| RA | 433,649 | T→G | 14.8% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 39.7% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 502,887 | T→A | 9.7% | I118F (ATC→TTC) | ybaL ← | inner membrane putative NAD(P)‑binding transporter |
| RA | 509,371 | A→C | 14.6% | V670G (GTG→GGG) | copA ← | copper transporter |
| RA | 524,899 | A→C | 7.5% | T547P (ACC→CCC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 599,579 | T→G | 24.4% | V289G (GTG→GGG) | cusA → | copper/silver efflux system, membrane component |
| RA | 599,612 | T→G | 20.1% | V300G (GTG→GGG) | cusA → | copper/silver efflux system, membrane component |
| RA | 649,766 | T→G | 15.7% | N242T (AAC→ACC) | citE ← | citrate lyase, citryl‑ACP lyase (beta) subunit |
| RA | 667,132 | A→C | 8.8% | G362G (GGT→GGG) | mrdA ← | penicillin‑binding protein 2, transpeptidase involved in peptidoglycan synthesis |
| RA | 705,630 | G→A | 8.7% | G563S (GGC→AGC) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 954,360 | T→A | 9.7% | Y36F (TAT→TTT) | focA ← | formate channel |
| RA | 989,945 | A→G | 18.2% | S138P (TCA→CCA) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,057,126 | C→G | 9.5% | A289G (GCC→GGC) | torT → | periplasmic sensory protein associated with the TorRS two‑component regulatory system |
| RA | 1,196,305 | C→T | 44.8% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| 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 | 1,377,689 | T→A | 8.4% | D286E (GAT→GAA) | ycjS → | putative NADH‑binding oxidoreductase |
| RA | 1,456,663 | A→G | 15.6% | G78G (GGA→GGG) | paaE → | ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component |
| RA | 1,466,201 | T→C | 7.0% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,210 | G→A | 5.8% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,856 | A→G | 5.5% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,504,667 | T→G | 21.9% | C317W (TGT→TGG) | insQ → | IS609 transposase B |
| RA | 1,542,110 | A→G | 20.7% | S161P (TCC→CCC) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,575,950 | A→T | 7.7% | I557N (ATC→AAC) | yddB ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,705,890 | G→A | 8.0% | G42R (GGG→AGG) | rsxA → | SoxR iron‑sulfur cluster reduction factor component; inner membrane protein of electron transport complex |
| RA | 1,708,709 | T→C | 9.7% | R597R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,798,500 | T→G | 10.3% | H148P (CAC→CCC) | pheS ← | phenylalanine tRNA synthetase, alpha subunit |
| 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 | 2,147,733 | T→G | 13.5% | G20G (GGT→GGG) | yegD → | Hsp70 chaperone family protein |
| RA | 2,149,907 | A→C | 19.3% | V360G (GTG→GGG) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| RA | 2,151,689 | G→T | 27.6% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| RA | 2,151,691 | C→T | 16.2% | intergenic (+45/+20) | 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 | 2,361,337 | A→C | 19.4% | G26G (GGT→GGG) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,521,126 | A→C | 10.5% | noncoding (76/76 nt) | valX → | tRNA‑Val |
| JC JC | 2,536,312 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | 62.8% | coding (479‑484/510 nt) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,793,675 | T→G | 8.4% | V314G (GTG→GGG) | gabT → | 4‑aminobutyrate aminotransferase, PLP‑dependent |
| RA | 2,807,369 | A→C | 18.3% | T80P (ACC→CCC) | proX → | glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein |
| RA | 2,828,506 | T→G | 12.3% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 2,978,166 | T→A | 14.2% | Y245F (TAT→TTT) | lysA ← | diaminopimelate decarboxylase, PLP‑binding |
| RA | 3,006,561 | T→C | 16.0% | A100A (GCT→GCC) | ygeW → | putative carbamoyltransferase |
| RA | 3,031,777 | A→C | 10.5% | P137P (CCA→CCC) | uacT → | uric acid permease |
| RA | 3,182,601 | G→T | 17.3% | G18C (GGC→TGC) | zupT → | zinc transporter |
| RA | 3,206,438 | G→A | 17.2% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,471 | C→G | 14.2% | S3R (AGC→AGG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,476 | G→A | 12.4% | S5N (AGT→AAT) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,477 | T→A | 16.4% | S5R (AGT→AGA) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,483 | G→A | 32.3% | K7K (AAG→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,487 | C→A | 14.7% | Q9K (CAG→AAG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,285,877 | C→G | 13.3% | P134A (CCG→GCG) | agaD → | N‑acetylgalactosamine‑specific enzyme IID component of PTS |
| RA | 3,370,875 | A→C | 18.4% | G54G (GGT→GGG) | nanE ← | putative N‑acetylmannosamine‑6‑P epimerase |
| 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 | 3,615,865 | A→C | 20.1% | T209P (ACC→CCC) | nikB → | nickel ABC transporter permease |
| RA | 3,731,689 | C→A | 12.0% | Q187K (CAA→AAA) | xylF → | D‑xylose transporter subunit |
| RA | 3,745,397 | A→C | 22.2% | L198F (TTA→TTC) | yiaN → | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| RA | 3,760,389 | A→C | 14.5% | S287R (AGT→AGG) | selA ← | selenocysteine synthase |
| RA | 3,781,966 | A→C | 14.9% | G199G (GGT→GGG) | cysE ← | serine acetyltransferase |
| RA | 3,782,913 | A→C | 18.9% | V250G (GTG→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| RA | 3,784,900 | A→C | 10.7% | V39G (GTG→GGG) | yibN ← | putative rhodanese‑related sulfurtransferase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,862,661 | T→G | 27.8% | 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 | 3,862,670 | T→A | 24.9% | 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 | 3,971,106 | T→G | 13.0% | V325G (GTA→GGA) | wecB → | UDP‑N‑acetyl glucosamine‑2‑epimerase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,027,146 | C→G | 12.1% | A207G (GCG→GGG) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,027,170 | G→T | 12.3% | C215F (TGC→TTC) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,098,391 | A→C | 18.9% | Y219S (TAC→TCC) | rhaS → | transcriptional activator of rhaBAD and rhaT |
| RA | 4,114,890 | A→C | 10.0% | G230G (GGT→GGG) | glpX ← | fructose 1,6‑bisphosphatase II |
| RA | 4,116,197 | A→C | 12.4% | G342G (GGT→GGG) | glpK ← | glycerol kinase |
| RA | 4,142,658 | C→G | 6.9% | G43G (GGC→GGG) | frwC → | putative enzyme IIC component of PTS |
| RA | 4,145,071 | A→C | 8.8% | Q359H (CAA→CAC) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,151,329 | T→G | 14.1% | A590A (GCA→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,160,854 | C→T | 59.8% | intergenic (‑64/‑270) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,161,139 | C→A | 9.7% | Q6K (CAA→AAA) | fabR → | transcriptional repressor of fabA and fabB |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 15.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 19.4% | 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 | 4,342,035 | A→C | 16.4% | D42A (GAC→GCC) | melA → | alpha‑galactosidase, NAD(P)‑binding |
| RA | 4,421,192 | A→G | 12.0% | S405G (AGT→GGT) | ulaA → | L‑ascorbate‑specific enzyme IIC permease component of PTS |
| RA | 4,430,023 | C→G | 12.8% | P54A (CCG→GCG) | cycA → | D‑alanine/D‑serine/glycine transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423828–3424233 | 3424468–3424241 | 9–641 | 68 [63] | [64] 74 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233730 | 4235475 | 1746 | 66 [63] | [64] 65 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1040547 = | NA (NA) | 5 (0.030) | 5/410 | NT | NA | noncoding (5/36 nt) | REP89 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP89 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | 1040579 = | NA (NA) | intergenic (+42/‑38) | cbdX/appA | putative cytochrome bd‑II oxidase subunit/phosphoanhydride phosphorylase | |||||
| * | ? | NC_000913 | 1207790 = | 28 (0.180) | 120 (0.830) | 68/398 | NT | 83.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 23 (0.160) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 27 (0.170) | 153 (1.060) | 86/398 | NT | 86.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 23 (0.160) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 55 (0.360) | 42/422 | 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 | = 1828681 | 100 (0.640) | 5 (0.030) | 5/412 | NT | 5.1% | coding (1054/1479 nt) | astD | succinylglutamic semialdehyde dehydrogenase |
| ? | NC_000913 | = 1828695 | 91 (0.610) | coding (1040/1479 nt) | astD | succinylglutamic semialdehyde dehydrogenase | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 72 (0.480) | 53/414 | 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 | = 2290113 | NA (NA) | 11 (0.070) | 10/430 | NT | 7.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2313352 = | 146 (0.940) | intergenic (+176/‑136) | micF/rcsD | sRNA antisense regulator affecting ompF expression, Hfq‑dependent/phosphotransfer intermediate protein in two‑component regulatory system with RcsBC | |||||
| * | ? | NC_000913 | 3619919 = | NA (NA) | 3 (0.020) | 3/424 | NT | 100% | coding (728/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3619966 = | 0 (0.000) | coding (775/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 4593324 = | NA (NA) | 5 (0.030) | 5/408 | NT | NA | intergenic (+12/+37) | tsr/lgoT | methyl‑accepting chemotaxis protein I, serine sensor receptor/putative L‑galactonate:H+ symporter |
| ? | NC_000913 | 4593354 = | NA (NA) | intergenic (+42/+7) | tsr/lgoT | methyl‑accepting chemotaxis protein I, serine sensor receptor/putative L‑galactonate:H+ symporter | |||||