mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.30.0 revision f53f5bf51c1f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 101,138 | C→T | 7.9% | A125V (GCC→GTC) | murC → | UDP‑N‑acetylmuramate:L‑alanine ligase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 300,196 | A→G | 100% | F247L (TTC→CTC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 323,369 | G→A | 86.3% | V344V (GTG→GTA) | ykgF → | ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component |
| RA | 463,152 | C→T | 5.3% | A413V (GCC→GTC) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 731,077 | A→G | 8.5% | T499A (ACT→GCT) | rhsC → | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 774,705 | Δ1 bp | 7.5% | intergenic (+103/‑47) | ybgE → / → ybgC | putative inner membrane protein in cydABX‑ybgE operon/acyl‑CoA thioester hydrolase |
| RA | 791,937 | A→G | 71.5% | V40A (GTA→GCA) | galE ← | UDP‑galactose‑4‑epimerase |
| RA | 884,387 | A→G | 7.0% | I239V (ATC→GTC) | mdfA → | multidrug efflux system protein |
| RA | 1,055,493 | G→A | 84.8% | A229V (GCA→GTA) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,097,158 | C→T | 13.3% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| JC | 1,326,599 | Δ36 bp | 9.1% | coding (1854‑1889/1896 nt) | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,394,129 | (A)5→4 | 100% | coding (903/1614 nt) | mppA → | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,708,847 | G→A | 8.1% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,756,826 | G→A | 61.3% | A377T (GCT→ACT) | pykF → | pyruvate kinase I |
| RA | 1,785,485 | T→C | 8.4% | E543G (GAG→GGG) | ppsA ← | phosphoenolpyruvate synthase |
| RA | 1,930,894 | G→A | 57.2% | G5D (GGC→GAC) | purT → | phosphoribosylglycinamide formyltransferase 2 |
| RA | 1,987,038 | C→T | 61.2% | G38G (GGC→GGT) | ftnB → | ferritin B, putative ferrous iron reservoir |
| RA | 2,096,876 | T→C | 59.3% | V88A (GTG→GCG) | hisI → | phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase |
| RA | 2,173,359 | Δ1 bp | 5.2% | pseudogene (4/442 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 | 2,173,363 | Δ2 bp | 100% | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,216,634 | T→C | 6.2% | E258E (GAA→GAG) | yehX ← | putative ABC transporter ATPase |
| RA | 2,230,157 | G→A | 90.0% | L77L (CTG→TTG) | dusC ← | tRNA‑dihydrouridine synthase C |
| RA | 2,304,840 | G→A | 7.3% | intergenic (+447/+268) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,349,267 | T→C | 7.9% | E69G (GAG→GGG) | inaA ← | acid‑inducible Kdo/WaaP family putative kinase |
| RA | 2,426,060 | A→G | 72.1% | G243G (GGT→GGC) | hisJ ← | histidine ABC transporter periplasmic binding protein |
| RA | 2,502,577 | G→A | 78.3% | P637S (CCG→TCG) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,528,975 | T→C | 8.1% | E401G (GAG→GGG) | ligA ← | DNA ligase, NAD(+)‑dependent |
| RA | 2,741,390 | G→A | 5.9% | A11T (GCT→ACT) | yfiL → | lipoprotein |
| RA | 2,756,933 | G→A | 74.5% | E259K (GAG→AAG) | intA → | CP4‑57 prophage; integrase |
| RA | 2,757,236 | G→A | 77.6% | A360T (GCG→ACG) | intA → | CP4‑57 prophage; integrase |
| RA | 2,810,153 | Δ1 bp | 100% | coding (537/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 3,017,043 | G→A | 5.7% | L328L (CTG→CTA) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,119,481 | T→C | 5.2% | intergenic (‑369/+116) | sslE ← / ← glcA | putative secreted and surface‑associated lipoprotein mucinase/glycolate transporter |
| RA | 3,120,887 | T→C | 9.0% | G131G (GGA→GGG) | glcA ← | glycolate transporter |
| RA | 3,198,419 | G→A | 6.8% | A408V (GCG→GTG) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,233,180 | A→G | 11.0% | I506V (ATT→GTT) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,233,246 | T→G | 8.2% | F528V (TTC→GTC) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,285,121 | T→C | 5.4% | L146P (CTC→CCC) | agaC → | N‑acetylgalactosamine‑specific enzyme IIC component of PTS |
| RA | 3,305,873 | A→G | 75.5% | intergenic (‑56/+98) | mtr ← / ← deaD | tryptophan transporter of high affinity/ATP‑dependent RNA helicase |
| RA | 3,349,497 | G→T | 10.8% | H105N (CAC→AAC) | mtgA ← | biosynthetic peptidoglycan transglycosylase |
| RA | 3,427,383 | A→C | 100% | noncoding (1380/1542 nt) | rrsD ← | 16S ribosomal RNA of rrnD operon |
| RA | 3,495,038 | C→A | 10.5% | A343E (GCA→GAA) | nirB → | nitrite reductase, large subunit, NAD(P)H‑binding |
| 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 | 3,748,468 | T→C | 73.5% | L462P (CTG→CCG) | lyxK → | L‑xylulose kinase |
| RA | 3,815,810 | Δ1 bp | 100% | intergenic (‑42/+24) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,848,173 | T→C | 11.0% | E151G (GAG→GGG) | uhpC ← | membrane protein regulates uhpT expression |
| RA | 3,895,657 | T→C | 6.0% | E318G (GAG→GGG) | adeP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,951,559:1 | +A | 91.5% | pseudogene (18/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,951,559:1 | +C | 6.0% | pseudogene (18/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,982,684:1 | (C)8→9 | 100% | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,016,542 | A→T | 5.2% | M38L (ATG→TTG) | udp → | uridine phosphorylase |
| RA | 4,085,480 | C→A | 7.3% | A115S (GCG→TCG) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,171,897 | A→G | 17.9% | intergenic (+141/‑160) | rrfB → / → murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| RA | 4,187,507 | A→C | 100% | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,204,398 | A→G | 7.2% | E360G (GAG→GGG) | zraR → | fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein |
| RA | 4,239,245:1 | (G)5→6 | 100% | coding (1612/2097 nt) | yjbH → | DUF940 family extracellular polysaccharide protein |
| RA | 4,296,190 | A→G | 23.0% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 26.0% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 22.4% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 13.7% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:2 | +G | 94.4% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,382:1 | +C | 100% | intergenic (+588/+54) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| JC | 4,397,624 | (GCTGGC)3→2 | 92.9% | coding (213‑218/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 720782 | 721175 | 394 | 74 [72] | [73] 74 | [ybfK]–[kdpE] | [ybfK], [kdpE] |
| * | * | ÷ | NC_000913 | 1978431 | 1979711 | 1281 | 74 [68] | [72] 76 | insB1–insA | insB1, insA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 279163 = | NA (NA) | 99 (0.650) | 6/530 | NT | 50.8% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2760086 | 96 (0.630) | coding (1102/1410 nt) | yfjI | CP4‑57 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | = 286650 | 113 (0.740) | 6 (0.040) | 6/510 | NT | 5.2% | coding (1256/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter |
| ? | NC_000913 | = 286682 | 109 (0.740) | coding (1288/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter | |||||
| * | ? | NC_000913 | 1207790 = | 79 (0.520) | 84 (0.580) | 63/498 | NT | 55.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 61 (0.420) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 77 (0.500) | 65 (0.450) | 52/498 | NT | 49.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 61 (0.420) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 48 (0.320) | 41/522 | 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) | 55 (0.370) | 45/514 | 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 | 3583428 = | NA (NA) | 29 (0.190) | 4/530 | NT | 26.1% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4507639 | 82 (0.540) | noncoding (1041/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 4325848 = | NA (NA) | 13 (0.090) +GGTGCCGAC |
5/512 | NT | NA | noncoding (47/583 nt) | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913 | = 4326338 | NA (NA) | noncoding (537/583 nt) | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913 | 4542682 = | 18 (0.120) | 3 (0.020) | 3/512 | NT | 5.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 82 (0.560) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||