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 | 4,530 | T→G | 11.3% | V266G (GTG→GGG) | thrC → | L‑threonine synthase |
| RA | 4,544 | G→T | 10.8% | A271S (GCT→TCT) | thrC → | L‑threonine synthase |
| RA | 200,112 | T→G | 9.7% | Y729D (TAT→GAT) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 284,003 | A→G | 15.3% | E268G (GAG→GGG) | yagF → | CP4‑6 prophage; dehydratase family protein |
| RA | 337,543 | T→C | 13.7% | S256P (TCC→CCC) | yahF → | putative NAD(P)‑binding succinyl‑CoA synthase |
| RA | 353,610 | C→G | 10.4% | A302G (GCG→GGG) | prpE → | propionate‑‑CoA ligase |
| RA | 360,362 | T→G | 15.3% | V124G (GTG→GGG) | cynX → | putative cyanate transporter |
| RA | 372,640 | T→G | 19.9% | L176V (TTA→GTA) | mhpD → | 2‑keto‑4‑pentenoate hydratase |
| RA | 385,818 | T→G | 17.2% | V196G (GTC→GGC) | tauA → | taurine ABC transporter periplasmic binding protein |
| RA | 395,289 | A→C | 12.3% | G333G (GGT→GGG) | ampH ← | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase; penicillin‑binding protein; weak beta‑lactamase |
| RA | 433,649 | T→G | 18.8% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 33.3% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 509,371 | A→C | 17.4% | V670G (GTG→GGG) | copA ← | copper transporter |
| RA | 596,493 | C→G | 8.5% | G298G (GGC→GGG) | cusC → | copper/silver efflux system, outer membrane component |
| RA | 766,690 | T→A | 16.0% | L236H (CTC→CAC) | mngA → | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 827,507 | T→G | 35.9% | D492A (GAC→GCC) | ybhF ← | putative ABC transporter ATPase |
| RA | 891,022 | A→G | 12.7% | E37G (GAG→GGG) | ybjC → | DUF1418 family protein |
| RA | 1,196,305 | C→T | 23.2% | 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 | 1,456,702 | T→G | 15.4% | G91G (GGT→GGG) | paaE → | ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,040,157 | A→G | 19.4% | K227R (AAG→AGG) | 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 | 31.7% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| RA | 2,151,691 | C→T | 19.1% | 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 | 2,228,310 | G→C | 11.3% | pseudogene (300/1287 nt) | mdtQ ← | pseudogene; putative channel/filament proteins |
| RA | 2,244,139 | T→G | 15.0% | V77G (GTG→GGG) | yeiG → | S‑formylglutathione hydrolase |
| JC JC | 2,536,312 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | 69.1% | coding (479‑484/510 nt) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,828,506 | T→G | 12.1% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 2,839,359 | T→G | 11.9% | intergenic (‑95/‑165) | ascG ← / → ascF | asc operon transcriptional repressor; prpBC operon repressor/cellobiose/arbutin/salicin‑specific PTS enzymes, IIB and IC components |
| RA | 3,080,691 | C→T | 12.0% | A315A (GCG→GCA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,206,438 | G→A | 18.3% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,456 | A→G | 11.7% | intergenic (‑200/‑7) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,471 | C→G | 15.6% | S3R (AGC→AGG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,477 | T→A | 18.4% | S5R (AGT→AGA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,484 | C→A | 13.8% | 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 | 17.5% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| 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 | 3,675,489 | T→G | 16.0% | V235G (GTG→GGG) | yhjE → | putative MFS transporter; membrane protein |
| RA | 3,716,989 | T→G | 12.8% | V148G (GTG→GGG) | yiaD → | multicopy suppressor of bamB; outer membrane lipoprotein |
| RA | 3,760,384 | A→C | 22.0% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| RA | 3,765,292 | T→A | 7.9% | I1037K (ATA→AAA) | rhsA → | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,781,954 | G→C | 10.0% | G203G (GGC→GGG) | cysE ← | serine acetyltransferase |
| RA | 3,781,966 | A→C | 12.3% | G199G (GGT→GGG) | cysE ← | serine acetyltransferase |
| RA | 3,782,917 | G→A | 21.5% | L249L (CTG→TTG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,830,356 | T→A | 14.1% | intergenic (+20/‑101) | xanP → / → yicH | xanthine permease/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,862,661 | T→G | 33.3% | 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 | 23.7% | 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 | 3,862,671 | C→A | 8.4% | pseudogene (933/1617 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 | 15.2% | 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 | 3,862,674 | C→A | 9.2% | pseudogene (930/1617 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 | 3,895,552 | A→C | 8.7% | V353G (GTG→GGG) | adeP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,952,815 | A→C | 7.8% | N111T (AAC→ACC) | ilvE → | branched‑chain amino acid aminotransferase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,027,132 | A→G | 17.8% | G202G (GGA→GGG) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,027,146 | C→G | 12.5% | A207G (GCG→GGG) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,160,854 | C→T | 65.4% | intergenic (‑64/‑270) | 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 | 4,228,164 | A→G | 13.1% | E145G (GAG→GGG) | yjbB → | putative Na+/Pi‑cotransporter |
| RA | 4,256,053 | G→C | 14.4% | G138G (GGC→GGG) | plsB ← | glycerol‑3‑phosphate O‑acyltransferase |
| RA | 4,256,085 | T→C | 10.4% | M128V (ATG→GTG) | plsB ← | glycerol‑3‑phosphate O‑acyltransferase |
| RA | 4,296,060 | C→T | 19.7% | intergenic (+266/+376) | 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 | 4,449,045 | T→G | 14.9% | intergenic (+3/+77) | chpB → / ← ppa | toxin of the ChpB‑ChpS toxin‑antitoxin system/inorganic pyrophosphatase |
| RA | 4,488,188 | A→G | 13.0% | M291V (ATG→GTG) | lptG → | lipopolysaccharide export ABC permease |
| RA | 4,488,192 | C→G | 10.9% | A292G (GCG→GGG) | lptG → | lipopolysaccharide export ABC permease |
| RA | 4,488,274 | C→T | 9.1% | F319F (TTC→TTT) | lptG → | lipopolysaccharide export ABC permease |
| RA | 4,536,218 | C→A | 23.8% | intergenic (+187/+396) | yjhR → / ← nanS | pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583065 | 583849 | 785 | 55 [53] | [52] 55 | [tfaX]–[appY] | [tfaX],[appY] |
| * | * | ÷ | NC_000913 | 1299450 | 1300748 | 1299 | 55 [54] | [54] 55 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 3804153 | 3805199 | 1047 | 60 [53] | [54] 55 | waaS–[waaP] | waaS,[waaP] |
| * | * | ÷ | NC_000913 | 4233742 | 4236053 | 2312 | 57 [51] | [50] 56 | pgi–[yjbE] | pgi,[yjbE] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 67363 | 96 (0.690) | 6 (0.050) | 5/408 | NT | 5.6% | coding (975/1503 nt) | araA | L‑arabinose isomerase |
| ? | NC_000913 | = 67394 | 111 (0.840) | coding (944/1503 nt) | araA | L‑arabinose isomerase | |||||
| * | ? | NC_000913 | = 741026 | NA (NA) | 3 (0.020) | 3/416 | NT | NA | noncoding (73/106 nt) | RIP66 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP66 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 741059 | NA (NA) | noncoding (106/106 nt) | RIP66 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP66 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 1207790 = | 22 (0.160) | 91 (0.710) | 62/398 | NT | 86.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.070) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.170) | 125 (0.970) | 74/398 | NT | 89.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.070) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 40 (0.290) | 35/422 | 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 | = 1978502 | 0 (0.000) | 45 (0.340) | 38/414 | 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 | = 2730108 | NA (NA) | 3 (0.020) | 3/420 | NT | NA | noncoding (1050/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 2730632 | NA (NA) | noncoding (526/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon | |||||