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 | 1,058 | C→T | 10.0% | P241L (CCC→CTC) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 7,573 | C→T | 6.3% | P129P (CCG→CCA) | yaaJ ← | putative transporter |
| RA | 114,506 | G→T | 5.9% | intergenic (+19/+16) | guaC → / ← hofC | GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein |
| RA | 114,507 | A→T | 5.9% | intergenic (+20/+15) | guaC → / ← hofC | GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein |
| RA | 114,510 | A→T | 6.1% | intergenic (+23/+12) | guaC → / ← hofC | GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein |
| RA | 114,511 | A→C | 6.3% | intergenic (+24/+11) | guaC → / ← hofC | GMP reductase/assembly protein in type IV pilin biogenesis, transmembrane protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 378,398 | A→G | 5.3% | intergenic (‑30/+64) | frmB ← / ← frmA | S‑formylglutathione hydrolase/alcohol dehydrogenase class III; glutathione‑dependent formaldehyde dehydrogenase |
| RA | 378,400 | G→A | 5.4% | intergenic (‑32/+62) | frmB ← / ← frmA | S‑formylglutathione hydrolase/alcohol dehydrogenase class III; glutathione‑dependent formaldehyde dehydrogenase |
| RA | 378,403 | T→C | 5.1% | intergenic (‑35/+59) | frmB ← / ← frmA | S‑formylglutathione hydrolase/alcohol dehydrogenase class III; glutathione‑dependent formaldehyde dehydrogenase |
| RA | 431,107 | A→T | 5.7% | intergenic (+155/+22) | yajD → / ← tsx | HNH nuclease family protein/nucleoside channel, receptor of phage T6 and colicin K |
| RA | 431,109 | A→T | 5.3% | intergenic (+157/+20) | yajD → / ← tsx | HNH nuclease family protein/nucleoside channel, receptor of phage T6 and colicin K |
| RA | 431,111 | A→T | 5.3% | intergenic (+159/+18) | yajD → / ← tsx | HNH nuclease family protein/nucleoside channel, receptor of phage T6 and colicin K |
| RA | 501,338 | G→T | 5.3% | S405I (AGC→ATC) | gsk → | inosine/guanosine kinase |
| RA | 513,502 | C→T | 5.1% | S309S (AGC→AGT) | ybaT → | putative amino acid transporter |
| RA | 598,102 | T→C | 5.5% | F208F (TTT→TTC) | cusB → | copper/silver efflux system, membrane fusion protein |
| RA | 632,070 | T→G | 6.4% | intergenic (+71/‑112) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 632,075 | G→A | 6.4% | intergenic (+76/‑107) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 632,076 | G→C | 6.3% | intergenic (+77/‑106) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 632,077 | T→C | 6.5% | intergenic (+78/‑105) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 632,082 | C→A | 6.6% | intergenic (+83/‑100) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 699,132 | C→G | 5.0% | E16Q (GAG→CAG) | asnB ← | asparagine synthetase B |
| RA | 699,134 | A→G | 5.0% | V15A (GTT→GCT) | asnB ← | asparagine synthetase B |
| RA | 1,183,882 | A→T | 5.4% | I188N (ATC→AAC) | potB ← | spermidine/putrescine ABC transporter permease |
| RA | 1,233,375 | G→A | 5.4% | T448M (ACG→ATG) | nhaB ← | sodium:proton antiporter |
| RA | 1,237,875 | T→C | 5.2% | M102T (ATG→ACG) | dadA → | D‑amino acid dehydrogenase |
| 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 |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,311,510 | C→T | 5.7% | A141V (GCA→GTA) | tonB → | membrane spanning protein in TonB‑ExbB‑ExbD transport complex |
| RA | 1,311,830 | A→G | 7.6% | intergenic (+22/+18) | tonB → / ← yciA | membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase |
| RA | 1,311,831 | C→T | 7.4% | intergenic (+23/+17) | tonB → / ← yciA | membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase |
| RA | 1,320,158 | C→T | 5.4% | G409G (GGG→GGA) | trpD ← | fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase |
| MC JC | 1,335,153 | Δ593 bp | 100% | [ymiA]–yciX | [ymiA], yciX | |
| RA | 1,337,334 | A→G | 5.4% | T502A (ACC→GCC) | acnA → | aconitate hydratase 1; aconitase A |
| RA | 1,400,366 | A→G | 6.0% | Y470H (TAC→CAC) | abgT ← | p‑aminobenzoyl‑glutamate transporter; membrane protein |
| RA | 1,429,024 | A→C | 6.2% | intergenic (+40/‑25) | lomR → / → stfR | pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein |
| RA | 1,457,286 | A→T | 6.0% | D286V (GAT→GTT) | paaE → | ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component |
| RA | 1,508,115 | C→A | 6.5% | D445E (GAC→GAA) | ydcP → | putative peptidase |
| RA | 1,525,613 | A→G | 5.8% | I123T (ATT→ACT) | ansP ← | L‑asparagine transporter |
| RA | 1,626,422 | T→A | 6.4% | Q320L (CAG→CTG) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 1,630,189 | C→T | 5.2% | G242D (GGT→GAT) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,708,854 | C→G | 22.0% | Q646E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,775,272 | C→T | 7.4% | A196V (GCC→GTC) | aroD → | 3‑dehydroquinate dehydratase |
| RA | 1,786,207 | C→T | 6.0% | L302L (CTG→CTA) | ppsA ← | phosphoenolpyruvate synthase |
| RA | 1,955,668 | C→G | 9.3% | G447A (GGT→GCT) | torZ ← | trimethylamine N‑oxide reductase system III, catalytic subunit |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 1,987,857 | C→T | 5.7% | intergenic (‑99/+16) | yecJ ← / ← azuC | DUF2766 family protein/acid‑inducible small membrane‑associated protein |
| RA | 1,987,858 | G→C | 6.4% | intergenic (‑100/+15) | yecJ ← / ← azuC | DUF2766 family protein/acid‑inducible small membrane‑associated protein |
| RA | 1,987,859 | G→C | 5.8% | intergenic (‑101/+14) | yecJ ← / ← azuC | DUF2766 family protein/acid‑inducible small membrane‑associated protein |
| RA | 1,987,860 | A→G | 5.9% | intergenic (‑102/+13) | yecJ ← / ← azuC | DUF2766 family protein/acid‑inducible small membrane‑associated protein |
| RA | 2,034,691 | G→A | 5.0% | pseudogene (641/663 nt) | yedS → | pseudogene, outer membrane protein homology; putative outer membrane protein |
| RA | 2,068,407 | A→G | 5.2% | pseudogene (13/159 nt) | yoeH ← | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related |
| RA | 2,068,408 | T→A | 5.4% | pseudogene (12/159 nt) | yoeH ← | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related |
| RA | 2,068,409 | G→C | 5.2% | pseudogene (11/159 nt) | yoeH ← | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related |
| RA | 2,068,410 | T→A | 5.4% | pseudogene (10/159 nt) | yoeH ← | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related |
| RA | 2,068,411 | C→T | 5.4% | pseudogene (9/159 nt) | yoeH ← | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,133,601 | C→T | 5.5% | E684E (GAG→GAA) | wzc ← | colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase |
| RA | 2,147,319 | A→T | 5.3% | C74* (TGT→TGA) | alkA ← | 3‑methyl‑adenine DNA glycosylase II |
| 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 | 2,219,632 | G→A | 6.2% | intergenic (‑151/+60) | osmF ← / ← bglX | putative ABC transporter periplasmic binding protein/beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,219,633 | C→A | 7.0% | intergenic (‑152/+59) | osmF ← / ← bglX | putative ABC transporter periplasmic binding protein/beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,357,689 | T→C | 7.8% | G262G (GGT→GGC) | yfaD → | transposase_31 family protein |
| RA | 2,407,898 | A→C | 5.8% | Q113P (CAG→CCG) ‡ | alaA → | glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| RA | 2,407,899 | G→T | 5.1% | Q113H (CAG→CAT) ‡ | alaA → | glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| RA | 2,560,985 | C→A | 17.2% | intergenic (+87/‑383) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,577,413 | A→G | 6.7% | L322P (CTG→CCG) | maeB ← | malic enzyme: putative oxidoreductase/phosphotransacetylase |
| RA | 2,800,515 | C→A | 5.6% | intergenic (+40/‑208) | ygaM → / → nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| RA | 2,800,517 | T→A | 8.0% | intergenic (+42/‑206) | ygaM → / → nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| RA | 2,800,519 | T→G | 7.5% | intergenic (+44/‑204) | ygaM → / → nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| RA | 2,836,188 | G→A | 5.2% | A413V (GCG→GTG) | hypF ← | carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein |
| RA | 2,849,789 | C→T | 5.5% | A21T (GCC→ACC) | hycB ← | hydrogenase 3, Fe‑S subunit |
| RA | 2,866,487 | G→C | 5.1% | intergenic (+22/+72) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,866,488 | G→C | 5.6% | intergenic (+23/+71) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,873,915 | A→G | 6.5% | H26H (CAT→CAC) ‡ | cysC ← | adenosine 5'‑phosphosulfate kinase |
| RA | 2,873,917 | G→C | 7.7% | H26D (CAT→GAT) ‡ | cysC ← | adenosine 5'‑phosphosulfate kinase |
| RA | 2,873,919 | C→T | 6.3% | G25D (GGT→GAT) | cysC ← | adenosine 5'‑phosphosulfate kinase |
| RA | 2,947,465 | Δ1 bp | 12.5% | intergenic (+2/‑32) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,947,467 | A→C | 12.7% | intergenic (+4/‑30) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 3,269,956 | T→A | 12.4% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,291,109 | A→T | 6.3% | K766* (AAA→TAA) ‡ | yraJ → | putative outer membrane protein |
| RA | 3,291,110 | A→T | 6.7% | K766I (AAA→ATA) ‡ | yraJ → | putative outer membrane protein |
| RA | 3,292,003 | G→A | 5.1% | S221S (TCG→TCA) | yraK → | putative fimbrial‑like adhesin protein |
| 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 |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,153,570 | G→A | 5.3% | intergenic (‑472/+126) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,285,313 | A→G | 5.1% | intergenic (‑100/+100) | yjcH ← / ← acs | DUF485 family inner membrane protein/acetyl‑CoA synthetase |
| RA | 4,285,320 | T→A | 5.1% | intergenic (‑107/+93) | yjcH ← / ← acs | DUF485 family inner membrane protein/acetyl‑CoA synthetase |
| RA | 4,285,321 | T→A | 5.1% | intergenic (‑108/+92) | yjcH ← / ← acs | DUF485 family inner membrane protein/acetyl‑CoA synthetase |
| RA | 4,285,327 | G→T | 6.1% | intergenic (‑114/+86) | yjcH ← / ← acs | DUF485 family inner membrane protein/acetyl‑CoA synthetase |
| RA | 4,285,328 | C→T | 6.1% | intergenic (‑115/+85) | yjcH ← / ← acs | DUF485 family inner membrane protein/acetyl‑CoA synthetase |
| RA | 4,296,060 | C→T | 35.5% | 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 | 4,391,330 | G→A | 5.0% | D60D (GAC→GAT) | rsgA ← | ribosome small subunit‑dependent GTPase A |
| RA | 4,394,953 | G→A | 5.9% | P296P (CCG→CCA) | nnr → | bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase |
| RA | 4,401,018 | G→A | 5.0% | R116H (CGT→CAT) | hflX → | GTPase, stimulated by 50S subunit binding; Mn(2+) homeostasis regulator |
| RA | 4,479,012 | A→T | 5.7% | intergenic (+123/+22) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,479,016 | G→C | 5.8% | intergenic (+127/+18) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,479,020 | A→T | 5.4% | intergenic (+131/+14) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,581,948 | C→T | 5.3% | Q367Q (CAG→CAA) | hsdM ← | DNA methyltransferase M |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 131579 | 134225 | 2647 | 39 [38] | [38] 39 | acnB | acnB |
| * | * | ÷ | NC_000913 | 3423758–3424234 | 3424535–3424238 | 5–778 | 39 [33] | [38] 40 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 381669 | NA (NA) | 3 (0.030) | 3/246 | NT | NA | noncoding (410/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381695 | NA (NA) | noncoding (436/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 35 (0.380) | 39 (0.480) | 32/228 | NT | 59.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 22 (0.270) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 34 (0.370) | 45 (0.560) | 40/228 | NT | 63.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 22 (0.270) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1396531 = | NA (NA) | 7 (0.080) | 6/248 | NT | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3128550 | 61 (0.660) | 4 (0.050) | 4/244 | NT | 6.2% | coding (279/765 nt) | glcC | glycolate‑inducible glc operon transcriptional repressor; autorepressor |
| ? | NC_000913 | = 3128567 | 64 (0.740) | coding (296/765 nt) | glcC | glycolate‑inducible glc operon transcriptional repressor; autorepressor | |||||
| * | ? | NC_000913 | = 4040727 | 83 (0.900) | 5 (0.060) | 5/242 | NT | 6.4% | intergenic (+91/+179) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913 | = 4171852 | 68 (0.790) | intergenic (+96/‑205) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding | |||||
| * | ? | NC_000913 | = 4171803 | 68 (0.740) | 10 (0.110) | 7/256 | NT | 10.8% | intergenic (+47/‑254) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | NC_000913 | = 4213162 | 99 (1.090) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||
| * | ? | NC_000913 | = 4542690 | 122 (1.320) | 15 (0.170) | 14/242 | NT | 11.1% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 126 (1.470) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||