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 | 175,537 | T→G | 26.2% | V144G (GTG→GGG) | clcA → | H(+)/Cl(‑) exchange transporter |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 429,830 | T→G | 17.1% | V109G (GTG→GGG) | secF → | SecYEG protein translocase auxillary subunit |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 42.2% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 550,033 | A→G | 14.3% | E136G (GAG→GGG) | ylbF → | putative anaerobic allantoin catabolic oxamate carbamoyltransferase; DUF2877 family protein |
| RA | 709,806 | T→C | 13.3% | L6P (CTC→CCC) | chiQ → | chitosugar‑induced verified lipoprotein |
| RA | 752,085 | G→A | 15.7% | L29F (CTC→TTC) | ybgQ ← | putative outer membrane protein |
| RA | 1,021,591 | T→G | 15.8% | C152G (TGT→GGT) | sxy → | CRP‑S‑dependent promoter expression factor |
| RA | 1,058,486 | T→C | 19.2% | S135P (TCG→CCG) | torC → | trimethylamine N‑oxide (TMAO) reductase I, cytochrome c‑type subunit |
| RA | 1,062,576 | G→A | 9.8% | L94F (CTT→TTT) | cbpM ← | modulator of CbpA co‑chaperone |
| RA | 1,196,131 | G→A | 28.5% | A337T (GCC→ACC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,305 | C→T | 55.3% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,286,612 | A→T | 17.4% | intergenic (+86/+454) | 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 | 1,630,551 | A→G | 11.3% | S121S (TCT→TCC) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,722,908 | T→C | 12.9% | L263P (CTC→CCC) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| RA | 1,825,226 | G→T | 15.6% | Q134K (CAG→AAG) | spy ← | periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| RA | 1,874,824 | C→G | 9.3% | T251T (ACG→ACC) | yeaM ← | putative DNA‑binding transcriptional regulator |
| RA | 1,877,287 | A→C | 21.5% | G82G (GGT→GGG) | yoaF ← | DUF333 family outer membrane lipoprotein |
| 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 | 2,173,361 | 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 | 2,260,629 | T→C | 20.2% | E261G (GAG→GGG) | fruA ← | fused fructose‑specific PTS enzymes: IIBcomponent/IIC components |
| RA | 2,303,243 | A→G | 14.5% | S85S (TCT→TCC) | napF ← | ferredoxin‑type protein, role in electron transfer to periplasmic nitrate reductase NapA |
| RA | 2,355,458 | T→G | 14.5% | G398G (GGT→GGG) | glpB → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase membrane anchor subunit |
| RA | 2,504,652 | A→C | 27.9% | V299G (GTG→GGG) | ypdE ← | aminopeptidase |
| RA | 2,748,341 | A→C | 12.8% | H127P (CAC→CCC) | ypjD → | cytochrome c assembly protein family inner membrane protein |
| RA | 2,791,798 | A→C | 21.8% | T176P (ACC→CCC) | gabD → | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| RA | 2,936,843 | T→C | 15.0% | S420S (TCT→TCC) | fucI → | L‑fucose isomerase |
| JC | 3,007,857 | +ACC | 9.2% | coding (348/1197 nt) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| RA | 3,051,839 | A→C | 13.8% | V160G (GTG→GGG) | ubiI ← | 2‑octaprenylphenol hydroxylase, FAD‑dependent |
| RA | 3,053,585 | T→G | 30.3% | N419T (AAC→ACC) | pepP ← | proline aminopeptidase P II |
| RA | 3,178,884 | A→G | 8.2% | E257G (GAG→GGG) | tolC → | transport channel |
| RA | 3,206,506 | C→A | 26.1% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,216,975 | T→G | 17.9% | V66G (GTG→GGG) | yqjI → | PadR family putative transcriptional regulator |
| RA | 3,287,639 | A→C | 17.1% | T72P (ACT→CCT) | yraH → | putative fimbrial‑like adhesin protein |
| RA | 3,289,010 | C→A | 11.1% | S66* (TCA→TAA) | yraJ → | putative outer membrane protein |
| RA | 3,293,687 | T→C | 17.9% | A96A (GCT→GCC) | lpoA → | OM lipoprotein stimulator of MrcA transpeptidase |
| RA | 3,300,864 | T→C | 14.9% | E138G (GAG→GGG) | yhbT ← | SCP‑2 sterol transfer family protein |
| RA | 3,376,876 | T→C | 9.2% | E182G (GAG→GGG) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,403,737 | T→C | 8.3% | L85P (CTC→CCC) | acuI → | putative acryloyl‑CoA reductase |
| RA | 3,414,310 | T→C | 17.6% | A149A (GCT→GCC) | acrE → | cytoplasmic membrane lipoprotein |
| RA | 3,463,240 | T→C | 12.0% | L106P (CTC→CCC) | gspK → | general secretory pathway component, cryptic |
| RA | 3,489,862 | A→G | 21.7% | S107P (TCC→CCC) | argD ← | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase |
| 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 | 15.8% | pseudogene (112/150 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,599,596 | A→G | 11.1% | A21A (GCT→GCC) | livJ ← | branched‑chain amino acid ABC transporter periplasmic binding protein |
| RA | 3,686,539 | T→C | 12.2% | S879G (AGC→GGC) | bcsC ← | cellulose synthase subunit |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,931,523 | A→C | 13.6% | T70P (ACC→CCC) | kup → | potassium transporter |
| RA | 3,949,065 | T→C | 12.4% | E302G (GAG→GGG) | yifB ← | magnesium chelatase family protein and putative transcriptional regulator |
| RA | 4,001,389 | G→A | 5.4% | intergenic (‑333/‑37) | yigE ← / → corA | DUF2233 family protein/magnesium/nickel/cobalt transporter |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,057,716 | A→G | 8.2% | S107P (TCC→CCC) | glnA ← | glutamine synthetase |
| RA | 4,158,653 | T→G | 11.8% | V55G (GTG→GGG) | oxyR → | oxidative and nitrosative stress transcriptional regulator |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,219,539 | C→T | 11.4% | A315V (GCG→GTG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,228,797 | T→G | 12.7% | V356G (GTG→GGG) | yjbB → | putative Na+/Pi‑cotransporter |
| RA | 4,295,700 | T→G | 19.9% | V407G (GTG→GGG) | gltP → | glutamate/aspartate:proton symporter |
| RA | 4,296,060 | C→T | 31.0% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 11.9% | 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 | 4,359,249 | A→C | 17.5% | S261R (AGT→AGG) | cadB ← | putative lysine/cadaverine transporter |
| RA | 4,430,345 | A→G | 13.9% | E161G (GAG→GGG) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,502,756 | C→T | 19.2% | E226K (GAA→AAA) | insG ← | IS4 transposase |
| RA | 4,587,589 | A→G | 14.0% | E214G (GAG→GGG) | mrr → | methylated adenine and cytosine restriction protein |
| RA | 4,606,902 | A→G | 21.7% | S267P (TCC→CCC) | rsmC ← | 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent |
| RA | 4,614,208 | A→G | 20.4% | E243G (GAG→GGG) | yjjV → | putative DNase |
| RA | 4,614,395 | T→C | 8.2% | intergenic (+135/+285) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,614,402 | C→T | 8.3% | intergenic (+142/+278) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2470094 | 2470453 | 360 | 20 [15] | [16] 20 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 4233755 | 4235439 | 1685 | 17 [16] | [16] 18 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 291401 | NA (NA) | 6 (0.080) | 6/426 | NT | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1293032 = | 0 (0.000) | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 22 (0.310) | 68 (1.040) | 50/394 | NT | 85.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 3 (0.050) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1207796 = | 22 (0.310) | 3 (0.040) +C |
3/424 | NT | 18.8% | coding (296/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209614 = | 4 (0.060) | pseudogene (6/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 22 (0.310) | 78 (1.190) | 52/394 | NT | 87.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 3 (0.050) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 28 (0.400) | 25/418 | 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) | 39 (0.570) | 32/410 | 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 | = 2852113 | 45 (0.640) | 3 (0.040) | 3/410 | NT | 6.1% | coding (250/273 nt) | hypC | hydrogenase maturation protein |
| ? | NC_000913 | = 2852157 | 49 (0.720) | coding (22/1122 nt) | hypD | hydrogenase maturation protein | |||||