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 | 69,740 | C→T | 5.3% | A103A (GCG→GCA) | araB ← | L‑ribulokinase |
| RA | 192,579 | A→T | 5.3% | *242L (TAA→TTA) | pyrH → | uridylate kinase |
| RA | 201,032 | G→A | 5.4% | G21D (GGC→GAC) | lpxD → | UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase |
| RA | 231,959 | G→T | 5.2% | G12C (GGC→TGC) | yafE → | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| RA | 231,964 | T→A | 5.4% | A13A (GCT→GCA) | yafE → | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 360,234 | G→T | 5.4% | M81I (ATG→ATT) | cynX → | putative cyanate transporter |
| RA | 473,813 | C→A | 14.7% | A283E (GCG→GAG) | amtB → | ammonium transporter |
| RA | 481,225 | T→G | 6.1% | intergenic (‑517/+29) | tomB ← / ← acrB | Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein |
| RA | 580,830 | T→A | 5.6% | intergenic (‑385/‑4) | ylcI ← / → nohD | DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein |
| RA | 580,831 | G→A | 5.0% | intergenic (‑386/‑3) | ylcI ← / → nohD | DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein |
| RA | 857,576 | T→C | 6.1% | intergenic (+21/+220) | ybiT → / ← ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| RA | 857,578 | C→G | 6.1% | intergenic (+23/+218) | ybiT → / ← ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| RA | 857,580 | G→A | 6.1% | intergenic (+25/+216) | ybiT → / ← ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| RA | 892,020 | G→T | 5.2% | L18L (CTG→CTT) | rimK → | ribosomal protein S6 modification protein |
| RA | 902,798 | A→T | 5.3% | F64Y (TTC→TAC) | artI ← | arginine transporter subunit |
| RA | 1,075,518 | A→C | 5.7% | L1122R (CTC→CGC) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,231,594 | G→C | 7.3% | V137L (GTG→CTG) | umuC → | translesion error‑prone DNA polymerase V subunit; DNA polymerase activity |
| RA | 1,231,598:1 | +C | 6.0% | coding (413/1269 nt) | umuC → | translesion error‑prone DNA polymerase V subunit; DNA polymerase activity |
| RA | 1,231,603 | Δ1 bp | 6.1% | coding (418/1269 nt) | umuC → | translesion error‑prone DNA polymerase V subunit; DNA polymerase activity |
| RA | 1,231,608 | G→C | 8.2% | Q141H (CAG→CAC) | umuC → | translesion error‑prone DNA polymerase V subunit; DNA polymerase activity |
| RA | 1,321,616 | C→T | 5.6% | R444H (CGT→CAT) | trpE ← | component I of anthranilate synthase |
| JC JC | 1,335,759 | IS1 (–) +9 bp | 100% | intergenic (+301/‑64) | yciX → / → acnA | uncharacterized protein/aconitate hydratase 1; aconitase A |
| RA | 1,388,283 | C→T | 5.9% | intergenic (+22/+22) | tyrR → / ← tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| RA | 1,388,284 | A→T | 5.6% | intergenic (+23/+21) | tyrR → / ← tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| RA | 1,388,285 | A→G | 6.2% | intergenic (+24/+20) | tyrR → / ← tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| RA | 1,398,924 | A→C | 5.5% | G201G (GGT→GGG) | fnr ← | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor |
| RA | 1,413,964 | C→T | 5.2% | intergenic (‑37/+20) | ralR ← / ← recT | Rac prophage; restriction alleviation protein/Rac prophage; recombination and repair protein |
| RA | 1,413,966 | T→A | 5.3% | intergenic (‑39/+18) | ralR ← / ← recT | Rac prophage; restriction alleviation protein/Rac prophage; recombination and repair protein |
| RA | 1,413,968 | A→G | 5.2% | intergenic (‑41/+16) | ralR ← / ← recT | Rac prophage; restriction alleviation protein/Rac prophage; recombination and repair protein |
| RA | 1,458,572 | C→T | 7.9% | I103I (ATC→ATT) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,521,409 | C→T | 5.0% | A553T (GCA→ACA) | yncD ← | putative iron outer membrane transporter |
| RA | 1,602,734 | C→G | 5.8% | A415A (GCC→GCG) | lsrA → | autoinducer 2 import ATP‑binding protein |
| RA | 1,617,565 | A→G | 5.9% | T180A (ACC→GCC) | ydeA → | arabinose efflux transporter, arabinose‑inducible |
| RA | 1,629,435 | G→A | 8.5% | intergenic (+17/+18) | ydfZ → / ← ydfI | selenoprotein, function unknown/putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,629,436 | A→T | 7.9% | intergenic (+18/+17) | ydfZ → / ← ydfI | selenoprotein, function unknown/putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,629,437 | T→C | 8.1% | intergenic (+19/+16) | ydfZ → / ← ydfI | selenoprotein, function unknown/putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,631,200 | A→G | 5.0% | pseudogene (1086/1284 nt) | ydfJ ← | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein |
| RA | 1,662,350 | C→T | 100% | P599S (CCC→TCC) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,695,367 | T→C | 5.1% | Q235Q (CAA→CAG) | uidA ← | beta‑D‑glucuronidase |
| RA | 1,756,710 | T→C | 5.3% | V338A (GTG→GCG) | pykF → | pyruvate kinase I |
| RA | 1,816,642 | G→T | 6.2% | T165N (ACT→AAT) | chbG ← | chito‑oligosaccharide deacetylase |
| RA | 1,877,788 | A→T | 5.5% | Q25L (CAG→CTG) | yeaP → | diguanylate cyclase |
| RA | 1,896,468 | T→G | 7.9% | V100G (GTG→GGG) | nudL → | putative CoA pyrophosphohydrolase, weak 3‑phosphohydroxypyruvate phosphatase |
| RA | 1,944,241 | T→C | 6.2% | intergenic (+42/+105) | znuB → / ← ruvB | zinc ABC transporter permease/ATP‑dependent DNA helicase, component of RuvABC resolvasome |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,024,609 | T→G | 5.2% | intergenic (+18/+26) | rcsA → / ← dsrB | transcriptional regulator of colanic acid capsular biosynthesis/uncharacterized protein |
| RA | 2,024,612 | C→A | 5.5% | intergenic (+21/+23) | rcsA → / ← dsrB | transcriptional regulator of colanic acid capsular biosynthesis/uncharacterized protein |
| RA | 2,048,319 | Δ1 bp | 5.1% | coding (3382/7077 nt) | yeeJ → | putative adhesin |
| RA | 2,062,354 | T→A | 5.2% | intergenic (+19/+37) | asnV → / ← ldtA | tRNA‑Asn/L,D‑transpeptidase linking Lpp to murein |
| RA | 2,062,356 | C→A | 5.2% | intergenic (+21/+35) | asnV → / ← ldtA | tRNA‑Asn/L,D‑transpeptidase linking Lpp to murein |
| RA | 2,073,667 | T→C | 6.0% | V710A (GTC→GCC) | flu → | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,076,391 | C→A | 5.1% | T28T (ACC→ACA) | yeeS → | CP4‑44 prophage; putative DNA repair protein |
| RA | 2,087,771 | C→T | 5.7% | R163Q (CGG→CAG) | yeeY ← | LysR family putative transcriptional regulator |
| RA | 2,098,896 | T→A | 5.2% | N240Y (AAC→TAC) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| RA | 2,123,622 | T→A | 5.2% | H300L (CAC→CTC) | cpsB ← | mannose‑1‑phosphate guanyltransferase |
| RA | 2,123,625 | C→G | 5.4% | C299S (TGC→TCC) ‡ | cpsB ← | mannose‑1‑phosphate guanyltransferase |
| RA | 2,123,626 | A→C | 5.5% | C299G (TGC→GGC) ‡ | cpsB ← | mannose‑1‑phosphate guanyltransferase |
| RA | 2,123,633 | G→T | 5.3% | G296G (GGC→GGA) ‡ | cpsB ← | mannose‑1‑phosphate guanyltransferase |
| RA | 2,123,634 | C→G | 5.2% | G296A (GGC→GCC) ‡ | cpsB ← | mannose‑1‑phosphate guanyltransferase |
| RA | 2,123,637 | T→A | 5.4% | E295V (GAG→GTG) | cpsB ← | mannose‑1‑phosphate guanyltransferase |
| RA | 2,129,487 | T→C | 5.9% | N55S (AAT→AGT) | wcaE ← | putative glycosyl transferase |
| RA | 2,148,199 | C→T | 5.2% | L176L (CTG→TTG) | yegD → | Hsp70 chaperone family protein |
| RA | 2,149,479 | T→C | 5.8% | T503A (ACT→GCT) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| RA | 2,161,391 | G→A | 6.0% | P1002P (CCG→CCA) | mdtC → | multidrug efflux system, subunit C |
| 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 | 2,243,472 | T→C | 5.1% | M61V (ATG→GTG) | folE ← | GTP cyclohydrolase I |
| RA | 2,373,122 | T→G | 5.2% | Y77* (TAT→TAG) | arnF → | undecaprenyl phosphate‑alpha‑L‑ara4N exporter; flippase ArnEF subunit |
| RA | 2,419,364 | A→T | 5.2% | F142Y (TTC→TAC) | yfcE ← | phosphodiesterase activity on bis‑pNPP |
| RA | 2,549,548 | T→G | 5.0% | intergenic (+142/+98) | yfeW → / ← yfeX | penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity/porphyrinogen oxidase, cytoplasmic |
| RA | 2,549,555 | G→T | 5.2% | intergenic (+149/+91) | yfeW → / ← yfeX | penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity/porphyrinogen oxidase, cytoplasmic |
| RA | 2,549,556 | C→T | 5.0% | intergenic (+150/+90) | yfeW → / ← yfeX | penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity/porphyrinogen oxidase, cytoplasmic |
| RA | 2,550,448 | G→A | 5.5% | A33V (GCC→GTC) | yfeX ← | porphyrinogen oxidase, cytoplasmic |
| RA | 2,573,897 | A→G | 5.1% | W137R (TGG→CGG) | eutT ← | cobalamin adenosyltransferase involved in ethanolamine utilization |
| RA | 2,596,356 | Δ1 bp | 5.3% | coding (382/864 nt) | ypfJ ← | putative neutral zinc metallopeptidase |
| RA | 2,684,575 | G→A | 5.2% | S311S (TCC→TCT) | glyA ← | serine hydroxymethyltransferase |
| RA | 2,691,169 | A→T | 5.7% | noncoding (172/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,691,171 | T→A | 6.0% | noncoding (170/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,691,173 | A→T | 6.7% | noncoding (168/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,705,868 | A→T | 5.3% | I419I (ATT→ATA) | lepA ← | back‑translocating elongation factor EF4, GTPase |
| RA | 2,709,445 | T→C | 5.1% | R190G (AGG→GGG) | rpoE ← | RNA polymerase sigma E factor |
| RA | 2,878,822 | A→G | 6.0% | V11A (GTA→GCA) | ygbF ← | CRISPR adaptation ssRNA endonuclease |
| RA | 2,936,359 | T→A | 5.4% | V259D (GTT→GAT) | fucI → | L‑fucose isomerase |
| RA | 2,947,465 | Δ1 bp | 11.8% | intergenic (+2/‑32) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,971,146 | T→C | 5.5% | intergenic (+13/‑125) | ygdQ → / → ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| RA | 2,997,620 | C→T | 7.5% | intergenic (‑20/+72) | insC1 ← / ← ygeQ | IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant |
| RA | 2,997,622 | A→T | 6.8% | intergenic (‑22/+70) | insC1 ← / ← ygeQ | IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant |
| RA | 2,997,625 | A→G | 6.8% | intergenic (‑25/+67) | insC1 ← / ← ygeQ | IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant |
| RA | 3,216,188 | C→T | 5.2% | D102N (GAT→AAT) | yqjH ← | putative siderophore interacting protein |
| RA | 3,234,708 | T→A | 5.1% | intergenic (‑253/+31) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,269,956 | T→C | 11.9% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,030 | T→C | 24.3% | intergenic (+428/+186) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| 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 | 3,662,481 | C→A | 5.1% | H690N (CAC→AAC) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,708,293 | C→T | 6.5% | intergenic (‑588/+323) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,427 | G→A | 7.1% | intergenic (‑722/+189) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,428 | T→A | 7.8% | intergenic (‑723/+188) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,429 | T→C | 7.3% | intergenic (‑724/+187) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,925,547 | A→G | 5.1% | G29G (GGT→GGC) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 4,024,149 | T→A | 5.9% | L199Q (CTG→CAG) | tatD → | quality control of Tat‑exported FeS proteins; Mg‑dependent cytoplasmic DNase |
| RA | 4,175,146 | Δ1 bp | 100% | intergenic (‑120/‑242) | coaA ← / → thrU | pantothenate kinase/tRNA‑Thr |
| RA | 4,182,938 | A→C | 13.6% | E565A (GAA→GCA) | rpoB → | RNA polymerase, beta subunit |
| JC | 4,187,217 | +GAT | 41.5% | coding (1868/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,188,572 | C→A | 15.1% | R1075S (CGT→AGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,270,523 | C→A | 100% | L96M (CTG→ATG) | yjbQ → | thiamine phosphate synthase |
| RA | 4,296,060 | C→T | 26.0% | 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 | 4,306,072 | C→T | 5.7% | V176I (GTT→ATT) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| RA | 4,306,095 | C→T | 6.0% | R168H (CGT→CAT) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| RA | 4,307,294 | A→T | 8.6% | L169Q (CTG→CAG) | alsK ← | D‑allose kinase |
| RA | 4,307,298 | G→A | 7.7% | P168S (CCC→TCC) | alsK ← | D‑allose kinase |
| RA | 4,490,628 | A→G | 5.4% | M171T (ATG→ACG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 131582 | 134223 | 2642 | 36 [35] | [35] 37 | acnB | acnB |
| * | * | ÷ | NC_000913 | 3423761–3424234 | 3424574–3424238 | 5–814 | 36 [35] | [33] 36 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 32 (0.350) | 50 (0.630) | 42/230 | NT | 60.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 38 (0.480) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 27 (0.300) | 37 (0.460) | 28/230 | NT | 54.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 38 (0.480) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 112 (1.270) | 76/254 | 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 | 2070206 = | 56 (0.620) | 5 (0.060) | 5/250 | NT | 10.0% | noncoding (66/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2997620 = | 37 (0.430) | noncoding (72/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2539674 | NA (NA) | 4 (0.050) | 4/248 | NT | NA | intergenic (‑91/+43) | cysM/cysA | cysteine synthase B (O‑acetylserine sulfhydrolase B)/sulfate/thiosulfate transporter subunit |
| ? | NC_000913 | = 2539688 | NA (NA) | intergenic (‑105/+29) | cysM/cysA | cysteine synthase B (O‑acetylserine sulfhydrolase B)/sulfate/thiosulfate transporter subunit | |||||
| * | ? | NC_000913 | 4304575 = | 124 (1.370) | 6 (0.070) | 4/240 | NT | 5.3% | intergenic (‑172/+37) | ytcA/yjcS | putative inner membrane efflux pump‑associated DUF1656 family protein/metallo‑beta‑lactamase superfamily protein |
| ? | NC_000913 | 4304603 = | 102 (1.230) | intergenic (‑200/+9) | ytcA/yjcS | putative inner membrane efflux pump‑associated DUF1656 family protein/metallo‑beta‑lactamase superfamily protein | |||||
| * | ? | NC_000913 | 4542682 = | 93 (1.020) | 16 (0.190) | 14/244 | NT | 13.4% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 121 (1.430) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 99 (1.090) | 15 (0.180) | 15/244 | NT | 12.3% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 121 (1.430) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||