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 | 7,733 | T→G | 16.7% | N76T (AAC→ACC) | yaaJ ← | putative transporter |
| RA | 249,538 | T→G | 14.4% | pseudogene (533/1713 nt) | lfhA ← | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 312,169 | T→G | 11.4% | L20V (TTG→GTG) | ykgL → | uncharacterized protein |
| RA | 337,515 | T→C | 17.8% | D246D (GAT→GAC) | yahF → | putative NAD(P)‑binding succinyl‑CoA synthase |
| RA | 353,606 | A→G | 14.0% | M301V (ATG→GTG) | prpE → | propionate‑‑CoA ligase |
| RA | 353,673 | A→G | 12.2% | E323G (GAG→GGG) | prpE → | propionate‑‑CoA ligase |
| RA | 357,819 | G→C | 22.1% | A291G (GCG→GGG) | cynR ← | transcriptional activator of cyn operon; autorepressor |
| RA | 421,608 | T→G | 14.0% | V208G (GTG→GGG) | proY → | proline‑specific permease |
| RA | 423,056 | A→G | 12.5% | D180G (GAC→GGC) | malZ → | maltodextrin glucosidase |
| RA | 424,671 | T→G | 14.7% | H83P (CAC→CCC) | acpH ← | acyl carrier protein (ACP) phosphodiesterase; ACP hydrolyase |
| RA | 433,649 | T→G | 28.5% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 87.1% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| JC JC | 458,790 | IS186 (+) +6 bp :: Δ1 bp | 65.1% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| JC JC | 458,873 | IS5 (–) +4 bp | 22.6% | intergenic (+173/‑12) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 509,371 | A→C | 13.1% | V670G (GTG→GGG) | copA ← | copper transporter |
| RA | 599,612 | T→G | 19.1% | V300G (GTG→GGG) | cusA → | copper/silver efflux system, membrane component |
| RA | 630,153 | T→G | 12.4% | V87G (GTG→GGG) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 732,848 | T→G | 12.7% | V1089G (GTG→GGG) | rhsC → | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 989,943 | T→G | 26.8% | S138S (TCA→TCC) ‡ | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 989,945 | A→G | 31.5% | S138P (TCA→CCA) ‡ | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 989,953 | C→G | 9.6% | R135P (CGC→CCC) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,196,305 | C→T | 93.6% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,271,865 | G→T | 19.6% | intergenic (‑16/‑254) | chaA ← / → chaB | calcium/sodium:proton antiporter/cation transport regulator |
| 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 | 1,364,905 | T→G | 13.4% | V225G (GTG→GGG) | puuB → | gamma‑glutamylputrescine oxidoreductase |
| RA | 1,542,110 | A→G | 24.1% | S161P (TCC→CCC) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,553,994 | T→G | 14.8% | D559A (GAC→GCC) | maeA ← | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme |
| RA | 1,888,554 | T→C | 7.1% | E398G (GAA→GGA) | fadD ← | acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase) |
| RA | 1,936,308 | C→T | 34.6% | V3I (GTA→ATA) | zwf ← | glucose‑6‑phosphate 1‑dehydrogenase |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,040,129 | A→C | 19.1% | T218P (ACA→CCA) | yedY → | membrane‑anchored, periplasmic TMAO, DMSO reductase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,139,187 | T→G | 20.6% | V429G (GTG→GGG) | yegH → | inner membrane 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 | 2,228,229 | G→C | 17.6% | pseudogene (381/1287 nt) | mdtQ ← | pseudogene; putative channel/filament proteins |
| RA | 2,311,317 | Δ1 bp | 6.1% | coding (218/1056 nt) | apbE ← | putative thiamine‑synthetic flavin transferase lipoprotein |
| RA | 2,670,496 | T→C | 9.2% | L36P (CTC→CCC) | hcaF → | 3‑phenylpropionate dioxygenase, small (beta) subunit |
| RA | 2,792,078 | A→C | 16.0% | D269A (GAC→GCC) | gabD → | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| RA | 2,828,506 | T→G | 18.5% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 3,153,892 | T→C | 12.8% | Y110Y (TAT→TAC) | yghB → | general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter |
| RA | 3,206,438 | G→A | 19.0% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,456 | A→G | 11.4% | intergenic (‑200/‑7) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,469 | A→G | 8.5% | S3G (AGC→GGC) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,471 | C→G | 14.2% | S3R (AGC→AGG) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,477 | T→A | 19.5% | S5R (AGT→AGA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,484 | C→A | 13.1% | Q8K (CAA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,487 | C→A | 13.5% | Q9K (CAG→AAG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,491 | C→A | 15.4% | A10E (GCA→GAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,506 | C→A | 15.2% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,237,903 | T→G | 11.9% | V198G (GTG→GGG) | ygjR → | putative NAD(P)‑dependent dehydrogenase |
| RA | 3,293,716 | T→G | 9.3% | V106G (GTA→GGA) | lpoA → | OM lipoprotein stimulator of MrcA transpeptidase |
| RA | 3,440,080 | C→A | 8.8% | R317L (CGC→CTC) | rpoA ← | RNA polymerase, 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 | 3,611,448 | T→C | 14.7% | S96G (AGC→GGC) | yhhS ← | putative arabinose efflux transporter |
| RA | 3,697,740 | T→G | 10.2% | V428G (GTG→GGG) | bcsE → | cellulose production protein |
| RA | 3,714,370 | G→T | 6.2% | A675A (GCC→GCA) | bisC ← | biotin sulfoxide reductase |
| RA | 3,760,384 | A→C | 29.2% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| RA | 3,781,954 | G→C | 11.2% | G203G (GGC→GGG) | cysE ← | serine acetyltransferase |
| RA | 3,781,966 | A→C | 14.9% | G199G (GGT→GGG) | cysE ← | serine acetyltransferase |
| RA | 3,782,011 | A→C | 14.4% | G184G (GGT→GGG) | cysE ← | serine acetyltransferase |
| RA | 3,782,890 | A→C | 13.8% | S258A (TCG→GCG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| RA | 3,782,921 | G→C | 13.3% | G247G (GGC→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| RA | 3,786,542 | T→G | 13.4% | V428G (GTC→GGC) | gpmM → | phosphoglycero mutase III, cofactor‑independent |
| RA | 3,812,804 | T→G | 12.6% | V25G (GTG→GGG) | dfp → | fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC JC | 3,836,839 | IS5 (–) +4 bp | 34.7% | intergenic (+283/‑111) | yicT → / → setC | pseudogene/putative arabinose efflux transporter |
| RA | 3,862,616 | T→A | 10.0% | pseudogene (988/1617 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 | 3,862,661 | T→G | 20.3% | 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 | 3,862,662 | T→G | 27.6% | pseudogene (942/1617 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 | 13.3% | 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 | 3,879,062 | A→T | 15.7% | M353K (ATG→AAG) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,895,556 | T→C | 15.9% | M352V (ATG→GTG) | adeP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,975,383 | A→C | 10.6% | T80P (ACC→CCC) | wecE → | TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,004,470 | G→C | 11.2% | C76W (TGC→TGG) | yigI ← | 4HBT thioesterase family protein |
| RA | 4,027,132 | A→G | 17.7% | G202G (GGA→GGG) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,027,146 | C→G | 13.7% | A207G (GCG→GGG) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,027,178 | C→G | 11.0% | R218G (CGT→GGT) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,151,329 | T→G | 23.8% | A590A (GCA→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 18.5% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 10.9% | 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 | 4,325,948 | A→G | 8.2% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,571,180 | A→C | 19.5% | V132G (GTG→GGG) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423867–3424234 | 3424443–3424239 | 6–577 | 39 [33] | [34] 37 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233769 | 4235491 | 1723 | 48 [34] | [36] 38 | [pgi] | [pgi] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 11 (0.090) | 111 (0.930) | 76/400 | NT | 92.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 8 (0.070) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 12 (0.090) | 96 (0.810) | 66/400 | NT | 90.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 8 (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 (0.320) | 30/424 | 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) | 70 (0.570) | 48/416 | 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 | = 3493765 | NA (NA) | 4 (0.030) | 4/416 | NT | NA | noncoding (8/26 nt) | REP248 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP248 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | = 3493775 | NA (NA) | noncoding (18/26 nt) | REP248 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP248 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | 4338210 = | 71 (0.550) | 4 (0.030) | 3/416 | NT | 5.0% | intergenic (‑281/+44) | adiY/adiA | adi system transcriptional activator/arginine decarboxylase |
| ? | NC_000913 | 4338238 = | 83 (0.670) | intergenic (‑309/+16) | adiY/adiA | adi system transcriptional activator/arginine decarboxylase | |||||