mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 17,135 | T→C | 13.9% | intergenic (+129/‑354) | sokC → / → nhaA | sRNA antisense regulator blocking mokC, and hence hokC, translation/sodium‑proton antiporter |
| RA | 126,947 | G→T | 100% | R418L (CGT→CTT) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 164,620 | C→T | 11.8% | intergenic (+86/‑110) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 164,621 | A→G | 11.5% | intergenic (+87/‑109) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 234,876 | T→C | 10.7% | W21R (TGG→CGG) | yafS → | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 349,717 | T→C | 11.8% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 514,150 | C→T | 14.5% | A53V (GCA→GTA) | cueR → | copper‑responsive regulon transcriptional regulator |
| RA | 538,630 | C→A | 10.8% | A333D (GCC→GAC) | ybbW → | putative allantoin transporter |
| RA | 732,825 | C→T | 7.9% | S1081S (TCC→TCT) | rhsC → | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 805,315 | C→T | 9.0% | L605L (CTG→TTG) | ybhJ → | aconitase family protein |
| RA | 844,358 | C→T | 25.9% | G375S (GGT→AGT) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 890,350 | T→C | 22.7% | S88P (TCA→CCA) | ybjM → | inner membrane protein |
| RA | 1,299,142 | G→A | 12.8% | G182D (GGC→GAC) | ychE → | UPF0056 family inner membrane protein |
| RA | 1,311,830 | A→G | 11.7% | intergenic (+22/+18) | tonB → / ← yciA | membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase |
| RA | 1,413,542 | A→T | 100% | Y67N (TAT→AAT) | ydaC ← | DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein |
| RA | 1,464,290 | T→C | 7.6% | L251P (CTT→CCT) | paaX → | transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer |
| RA | 1,466,504 | A→G | 12.5% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,485,617 | C→A | 10.1% | H853N (CAT→AAT) | hrpA → | putative ATP‑dependent helicase |
| RA | 1,585,149 | Δ1 bp | 16.7% | coding (1338/2280 nt) | ydeP ← | putative oxidoreductase |
| RA | 1,585,156:1 | +C | 17.6% | coding (1331/2280 nt) | ydeP ← | putative oxidoreductase |
| RA | 1,679,735 | T→A | 14.9% | L60H (CTC→CAC) | ydgI → | putative arginine/ornithine antiporter transporter |
| RA | 1,793,897 | Δ1 bp | 100% | coding (213/552 nt) | btuE ← | glutathione peroxidase |
| RA | 1,867,661 | T→C | 8.5% | C252R (TGC→CGC) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,093,040 | G→A | 100% | A215T (GCT→ACT) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 2,231,088 | A→G | 15.0% | A24A (GCA→GCG) | yohK → | LrgB family inner membrane protein |
| RA | 2,731,071 | A→T | 10.0% | noncoding (85/1542 nt) | rrsG ← | 16S ribosomal RNA of rrnG operon |
| RA | 2,731,072 | A→T | 8.3% | noncoding (84/1542 nt) | rrsG ← | 16S ribosomal RNA of rrnG operon |
| RA | 2,746,100 | G→A | 11.6% | R28R (CGC→CGT) | rpsP ← | 30S ribosomal subunit protein S16 |
| RA | 2,814,858 | A→G | 13.0% | noncoding (59/78 nt) | micA → | sRNA antisense regulator of ompA, lamB, ompX, and phoP; Hfq‑dependent |
| RA | 2,814,859 | C→T | 11.1% | noncoding (60/78 nt) | micA → | sRNA antisense regulator of ompA, lamB, ompX, and phoP; Hfq‑dependent |
| RA | 2,832,517 | G→A | 12.9% | R15H (CGT→CAT) | norV → | anaerobic nitric oxide reductase flavorubredoxin |
| RA | 2,964,941 | A→G | 9.1% | Y71Y (TAT→TAC) | thyA ← | thymidylate synthetase |
| RA | 3,486,216 | G→T | 6.8% | Q33H (CAG→CAT) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| RA | 3,486,223 | A→T | 7.1% | K36* (AAA→TAA) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| RA | 3,486,769 | T→C | 7.7% | intergenic (+19/‑20) | crp → / → yhfK | cAMP‑activated global transcription factor, mediator of catabolite repression/putative transporter, FUSC superfamily inner membrane protein |
| RA | 3,486,774 | T→A | 9.3% | intergenic (+24/‑15) | crp → / → yhfK | cAMP‑activated global transcription factor, mediator of catabolite repression/putative transporter, FUSC superfamily inner membrane protein |
| RA | 3,486,779 | G→A | 9.7% | intergenic (+29/‑10) | crp → / → yhfK | cAMP‑activated global transcription factor, mediator of catabolite repression/putative transporter, FUSC superfamily inner membrane protein |
| RA | 3,598,439 | T→C | 12.2% | intergenic (+73/+115) | panM → / ← livJ | PanD autocleavage accelerator, panothenate synthesis/branched‑chain amino acid ABC transporter periplasmic binding protein |
| RA | 3,618,566 | C→T | 6.0% | T264T (ACC→ACT) | nikE → | nickel ABC transporter ATPase |
| RA | 3,623,585 | A→G | 100% | E63G (GAA→GGA) | yhhH → | putative NTF2 fold immunity protein for polymorphic toxin RhsB |
| RA | 3,704,843 | A→C | 8.2% | M316R (ATG→AGG) | dppB ← | dipeptide/heme ABC transporter permease |
| RA | 3,756,561:1 | +G | 8.0% | intergenic (‑51/+114) | aldB ← / ← yiaY | aldehyde dehydrogenase B/L‑threonine dehydrogenase |
| RA | 3,756,564 | Δ1 bp | 7.8% | intergenic (‑54/+111) | aldB ← / ← yiaY | aldehyde dehydrogenase B/L‑threonine dehydrogenase |
| RA | 3,790,302 | A→T | 8.4% | intergenic (‑222/+17) | waaH ← / ← tdh | LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,890,154 | C→T | 9.2% | intergenic (+10/‑81) | tnaA → / → tnaB | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/tryptophan transporter of low affinity |
| RA | 4,116,703 | T→G | 100% | K173N (AAA→AAC) | glpK ← | glycerol kinase |
| RA | 4,188,710 | T→C | 5.3% | L1121P (CTG→CCG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,235,468 | G→A | 6.5% | intergenic (+62/‑437) | pgi → / → yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,235,469 | C→A | 6.5% | intergenic (+63/‑436) | pgi → / → yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,235,476 | G→A | 6.3% | intergenic (+70/‑429) | pgi → / → yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,235,477 | T→C | 7.8% | intergenic (+71/‑428) | pgi → / → yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,235,484 | T→G | 7.0% | intergenic (+78/‑421) | pgi → / → yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,235,485 | T→C | 6.2% | intergenic (+79/‑420) | pgi → / → yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,325,821 | G→T | 5.7% | intergenic (‑79/+579) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,325,824 | A→C | 5.4% | intergenic (‑82/+576) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,360,900 | Δ1 bp | 10.0% | coding (1036/1539 nt) | cadC ← | cadBA operon transcriptional activator |
| RA | 4,365,453 | G→T | 7.5% | intergenic (‑96/+20) | cutA ← / ← dcuA | divalent‑cation tolerance protein, copper sensitivity/C4‑dicarboxylate antiporter |
| RA | 4,365,454 | A→C | 7.5% | intergenic (‑97/+19) | cutA ← / ← dcuA | divalent‑cation tolerance protein, copper sensitivity/C4‑dicarboxylate antiporter |
| RA | 4,366,856 | C→A | 11.5% | intergenic (‑82/+36) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,399,892 | A→C | 36.2% | I214L (ATT→CTT) | miaA → | delta(2)‑isopentenylpyrophosphate tRNA‑adenosine transferase |
| RA | 4,496,512 | A→G | 7.5% | intergenic (+22/‑164) | leuX → / → intB | tRNA‑Leu/pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase |
| RA | 4,496,513 | C→T | 6.8% | intergenic (+23/‑163) | leuX → / → intB | tRNA‑Leu/pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase |
| RA | 4,552,838 | Δ1 bp | 6.2% | intergenic (+17/‑64) | uxuA → / → uxuB | mannonate hydrolase/D‑mannonate oxidoreductase, NAD‑dependent |
| RA | 4,552,842:1 | +A | 6.2% | intergenic (+21/‑60) | uxuA → / → uxuB | mannonate hydrolase/D‑mannonate oxidoreductase, NAD‑dependent |
| RA | 4,552,846 | G→A | 6.2% | intergenic (+25/‑56) | uxuA → / → uxuB | mannonate hydrolase/D‑mannonate oxidoreductase, NAD‑dependent |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 366215 | 366404 | 190 | 9 [8] | [8] 9 | [lacZ] | [lacZ] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 481050 = | 31 (0.710) | 4 (0.090) | 4/276 | NT | 11.4% | intergenic (‑342/+204) | tomB/acrB | Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein |
| ? | NC_000913 | 1467910 = | NA (NA) | intergenic (+6/+11) | ydbA/insD1 | pseudogene, autotransporter homolog; interrupted by IS2 and IS30/IS2 transposase TnpB | |||||
| * | ? | NC_000913 | 1207790 = | 22 (0.500) | 12 (0.310) | 12/244 | NT | 35.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 24 (0.620) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 21 (0.480) | 15 (0.390) | 14/244 | NT | 41.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 24 (0.620) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 34 (0.800) | 30/268 | 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 | = 1469240 | NA (NA) | 31 (0.710) | 23/276 | NT | 100% | intergenic (‑91/‑1) | insC1/ydbA | IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| ? | NC_000913 | = 1652258 | 0 (0.000) | pseudogene (708/1158 nt) | intQ | pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1651547 | NA (NA) | 29 (0.670) | 26/274 | NT | 100% | intergenic (+10/‑4) | insD1/intQ | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related |
| ? | NC_000913 | 1652253 = | 0 (0.000) | pseudogene (703/1158 nt) | intQ | pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 2406857 = | 0 (0.000) | 39 (0.900) | 30/274 | NT | 100% | intergenic (‑218/‑702) | lrhA/alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| ? | NC_000913 | = 2997688 | NA (NA) | intergenic (‑90/+2) | insC1/ygeQ | IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant | |||||
| * | ? | NC_000913 | = 2406863 | 0 (0.000) | 42 (0.960) | 33/274 | NT | 100% | intergenic (‑224/‑696) | lrhA/alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| ? | NC_000913 | 2996360 = | NA (NA) | intergenic (‑2/+10) | ygeO/insD1 | pseudogene, orgA family, part of T3SS PAI ETT2 remnant/IS2 transposase TnpB | |||||
| * | ? | NC_000913 | 3186094 = | NA (NA) | 55 (1.250) | 41/276 | NT | 100% | intergenic (+6/‑91) | yqiG/insC1 | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA |
| ? | NC_000913 | 3485933 = | 0 (0.000) | intergenic (‑117/‑185) | yhfA/crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression | |||||
| * | ? | NC_000913 | = 3187424 | NA (NA) | 50 (1.140) | 37/276 | NT | 100% | intergenic (+11/‑1) | insD1/yqiG | IS2 transposase TnpB/pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | NC_000913 | = 3485937 | 0 (0.000) | intergenic (‑121/‑181) | yhfA/crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression | |||||
| * | ? | NC_000913 | 3583427 = | NA (NA) | 10 (0.230) | 8/276 | NT | 14.5% | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA |
| ? | NC_000913 | 3658812 = | 59 (1.350) | coding (448/528 nt) | gadE | gad regulon transcriptional activator | |||||
| * | ? | NC_000913 | = 4253999 | NA (NA) | 3 (0.070) | 3/262 | NT | NA | noncoding (100/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site |
| ? | NC_000913 | = 4254029 | NA (NA) | noncoding (130/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 4295973 = | 29 (0.660) | 6 (0.140) | 3/262 | NT | 17.9% | noncoding (140/602 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites |
| ? | NC_000913 | 4296067 = | NA (NA) | noncoding (234/602 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||