mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 147,213 | 2 bp→TT | coding (246‑247/903 nt) | rpnC → | recombination‑promoting nuclease RpnC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 299,490 | T→C | E482G (GAA→GGA) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 350,292 | G→A | R94H (CGT→CAT) | prpC → | 2‑methylcitrate synthase |
| RA | 364,170 | 2 bp→AA | coding (2135‑2136/3075 nt) | lacZ ← | beta‑galactosidase |
| RA | 447,538 | A→G | F56F (TTT→TTC) | cyoE ← | heme O synthase |
| RA | 460,060 | C→T | I391I (ATC→ATT) | lon → | Lon protease |
| RA | 475,884 | C→T | T169I (ACC→ATC) | ybaY → | PF09619 family lipoprotein YbaY |
| JC JC | 480,919 | IS2 (–) +5 bp | intergenic (‑211/+331) | tomB ← / ← acrB | Hha toxicity modulator TomB/multidrug efflux pump RND permease AcrB |
| JC JC | 481,030 | IS2 (–) +5 bp | intergenic (‑322/+220) | tomB ← / ← acrB | Hha toxicity modulator TomB/multidrug efflux pump RND permease AcrB |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| RA | 584,506 | C→T | intergenic (+76/+174) | appY → / ← ompT | DNA‑binding transcriptional activator AppY/omptin family outer membrane protease OmpT |
| JC JC | 585,707 | IS2 (+) +5 bp | intergenic (‑74/+436) | ompT ← / ← envY | omptin family outer membrane protease OmpT/DNA‑binding transcriptional activator EnvY |
| RA | 731,569 | C→T | R663W (CGG→TGG) | rhsC → | rhs element protein RhsC |
| RA | 782,011 | C→T | intergenic (+359/‑74) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase |
| RA | 789,579 | 2 bp→AA | coding (400‑401/1149 nt) | galK ← | galactokinase |
| RA | 911,369 | G→A | A261V (GCG→GTG) | hcr ← | NADH oxidoreductase |
| JC JC | 926,188 | IS2 (–) +5 bp | intergenic (‑217/+33) | serW ← / ← infA | tRNA‑Ser/translation initiation factor IF‑1 |
| RA | 928,622 | G→A | L192L (CTG→TTG) | cydC ← | glutathione/L‑cysteine ABC exporter subunit CydC |
| RA | 1,018,847 | G→A | Q121Q (CAG→CAA) | matP → | macrodomain Ter protein |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| JC JC | 1,228,095 | IS2 (+) +5 bp | coding (17‑21/660 nt) | ycgM → | putative isomerase/hydrolase |
| RA | 1,242,845 | G→A | A79V (GCC→GTC) | ldcA ← | murein tetrapeptide carboxypeptidase |
| RA | 1,300,881 | G→T | intergenic (+334/‑301) | insH21 → / → oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,477,804 | C→T | L62F (CTT→TTT) | ynbA → | CDP‑alcohol phosphatidyltransferase domain‑containing protein YnbA |
| RA | 1,605,953 | G→A | Q301Q (CAG→CAA) | lsrB → | Autoinducer‑2 ABC transporter periplasmic binding protein |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,671,143 | IS2 (+) +5 bp | intergenic (+191/‑229) | ynfM → / → asr | putative transporter YnfM/periplasmic chaperone Asr |
| RA | 1,713,873 | C→T | L369L (CTG→TTG) | dtpA → | dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,869,314 | G→A | S120S (TCG→TCA) | yeaH → | DUF444 domain‑containing protein YeaH |
| RA | 1,915,009 | G→A | Q176* (CAG→TAG) | proQ ← | RNA chaperone ProQ |
| RA | 1,985,932 | C→T | G66D (GGC→GAC) | araF ← | arabinose ABC transporter periplasmic binding protein |
| RA | 2,000,983 | Δ1 bp | coding (42/552 nt) | fliZ ← | DNA‑binding transcriptional regulator FliZ |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,039,555 | A→G | L26L (TTA→TTG) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,061,989 | T→C | intergenic (‑56/‑271) | nac ← / → asnV | DNA‑binding transcriptional dual regulator Nac/tRNA‑Asn |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,174,844 | IS5 (+) +4 bp | coding (203‑206/453 nt) | gatA ← | galactitol‑specific PTS enzyme IIA component |
| RA | 2,259,422 | A→C | intergenic (‑126/+297) | psuK ← / ← fruA | putative pseudouridine kinase/fructose‑specific PTS multiphosphoryl transfer protein FruA |
| RA | 2,268,985 | G→A | Q44Q (CAG→CAA) | lpxT → | lipid A‑core phosphotransferase |
| JC | 2,278,188 | (AGACCAGC)1→2 | coding (50/345 nt) | yejG ← | protein YejG |
| JC JC | 2,317,225 | IS2 (–) +5 bp | coding (2648‑2652/2850 nt) | rcsC ← | histidine kinase RcsC |
| RA | 2,422,263 | G→A | G186S (GGC→AGC) | yfcH → | epimerase family protein YfcH |
| JC JC | 2,448,586 | IS5 (–) +4 bp | intergenic (‑146/‑17) | prmB ← / → smrB | ribosomal protein L3 N(5)‑glutamine methyltransferase/putative endonuclease SmrB |
| RA | 2,474,885 | G→C | intergenic (+29/‑99) | yfdQ → / → yfdR | DUF2303 domain‑containing protein YfdQ/5'‑deoxynucleotidase |
| RA | 2,493,138 | G→A | P39P (CCC→CCT) | frc ← | formyl‑CoA transferase |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,629,583 | T→G | intergenic (+102/‑209) | yfgG → / → yfgH | nickel/cobalt stress response protein YfgG/lipoprotein YfgH |
| RA | 2,648,617 | T→C | D1224G (GAT→GGT) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,656,129 | C→T | G77D (GGT→GAT) | pepB ← | aminopeptidase B |
| RA | 2,681,500 | G→A | P416S (CCT→TCT) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,731,034 | G→A | noncoding (124/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 2,751,849 | G→A | D19N (GAT→AAT) | recN → | DNA repair protein RecN |
| JC | 2,765,463 | (TATGGCAC)6→7 | intergenic (‑310/+50) | abpA ← / ← yfjM | anti‑bacteriophage protein/protein YfjM |
| RA | 2,780,701 | T→C | N676D (AAT→GAT) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,811,848 | G→A | S141N (AGC→AAC) | emrA → | multidrug efflux pump membrane fusion protein EmrA |
| RA | 2,823,589 | G→A | R61C (CGT→TGT) | recA ← | DNA recombination/repair protein RecA |
| RA | 2,867,463 | A→C | L30* (TTA→TGA) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,873,316 | T→C | T8A (ACA→GCA) | ygbE ← | DUF3561 domain‑containing inner membrane protein YgbE |
| RA | 2,878,434 | G→A | intergenic (+816/+135) | iap → / ← cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| RA | 2,891,085 | G→A | P272S (CCG→TCG) | cysJ ← | sulfite reductase, flavoprotein subunit |
| RA | 2,903,727 | G→A | intergenic (+353/+1020) | ygcE → / ← queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 2,913,761 | G→A | L414L (CTG→TTG) | rlmD ← | 23S rRNA m(5)U1939 methyltransferase |
| RA | 2,930,364 | G→A | W263* (TGG→TGA) | sdaB → | L‑serine deaminase II |
| RA | 2,937,789 | G→A | A108T (GCA→ACA) | fucK → | L‑fuculokinase |
| MC JC | 2,942,775 | (GTTGTGTT)2→1 | noncoding (80‑87/206 nt) | gcvB → | small regulatory RNA GcvB |
| RA | 3,017,470 | C→T | P471S (CCG→TCG) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,032,832 | C→T | R6C (CGC→TGC) | yqfG → | uncharacterized protein YqfG |
| RA | 3,036,781 | G→A | F442F (TTC→TTT) | recJ ← | ssDNA‑specific exonuclease RecJ |
| RA | 3,039,623 | G→A | H41Y (CAT→TAT) | xerD ← | site‑specific recombinase |
| RA | 3,041,451 | G→A | A47T (GCA→ACA) | ygfZ → | folate‑binding protein |
| RA | 3,065,497 | G→A | Q232Q (CAG→CAA) | scpC → | propionyl‑CoA:succinate CoA transferase |
| JC JC | 3,252,952 | IS2 (–) +5 bp | coding (42‑46/357 nt) | yhaI → | putative inner membrane protein |
| JC JC | 3,262,484 | IS5 (–) +4 bp | coding (1174‑1177/1209 nt) | tdcD ← | propionate kinase |
| JC JC | 3,361,732 | IS5 (–) +4 bp | coding (557‑560/765 nt) | gltF → | periplasmic protein GltF |
| RA | 3,413,827 | G→A | intergenic (‑362/‑37) | envR ← / → acrE | DNA‑binding transcriptional repressor EnvR/multidrug efflux pump membrane fusion lipoprotein AcrE |
| RA | 3,474,290 | T→C | K88R (AAA→AGA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,572,319 | T→G | E395A (GAA→GCA) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,633,668 | T→A | intergenic (‑1078/‑1173) | yhiJ ← / → yhiM | DUF4049 domain‑containing protein YhiJ/inner membrane protein YhiM |
| JC JC | 3,725,990 | IS5 (–) +4 bp | coding (104‑107/996 nt) | wecH → | O‑acetyltransferase WecH |
| RA | 3,797,329 | C→T | L128L (CTA→TTA) | waaL → | O‑antigen ligase |
| JC | 3,888,720 | Δ6 bp | intergenic (+211/‑5) | tnaC → / → tnaA | tnaAB operon leader peptide/tryptophanase |
| JC JC | 3,939,062 | IS2 (+) +5 bp | coding (836‑840/993 nt) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| RA | 3,957,805 | G→A | L6L (CTG→TTG) | ilvY ← | DNA‑binding transcriptional dual regulator IlvY |
| RA | 3,971,703 | G→A | E148E (GAG→GAA) | wecC → | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| RA | 4,004,180 | G→A | intergenic (‑2/+50) | rarD ← / ← yigI | putative transporter RarD/putative thioesterase YigI |
| RA | 4,018,586 | G→A | L418L (CTG→CTA) | rmuC → | putative recombination limiting protein RmuC |
| RA | 4,149,535 | C→T | G244D (GGC→GAC) | eptC ← | phosphoethanolamine transferase EptC |
| RA | 4,216,329 | C→T | I284I (ATC→ATT) | aceB → | malate synthase A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,309,712 | C→T | W423* (TGG→TGA) | alsA ← | D‑allose ABC transporter ATP binding subunit |
| RA | 4,311,002 | 2 bp→GT | intergenic (‑22/+104) | alsA ← / ← alsB | D‑allose ABC transporter ATP binding subunit/D‑allose ABC transporter periplasmic binding protein |
| RA | 4,392,517 | G→A | noncoding (46/76 nt) | glyX → | tRNA‑Gly |
| RA | 4,515,556 | G→A | S374S (AGC→AGT) | fecA ← | ferric citrate outer membrane transporter |
| RA | 4,624,587 | G→A | S68L (TCA→TTA) | ytjB ← | putative inner membrane protein Smp |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 780630 | 780864 | 235 | 17 [0] | [2] 3 | valT–[lysW] | valT,[lysW] |
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 16 [0] | [0] 13 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423903–3424412 | 3424412 | 1–510 | 3 [2] | [2] 3 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4244447 | 4246870 | 2424 | 3 [2] | [2] 3 | [malF]–[malK] | [malF],malE,[malK] |
| * | * | ÷ | NC_000913 | 4247041 | 4249361 | 2321 | 3 [2] | [0] 42 | [malK]–lamB | [malK],lamB |
| * | * | ÷ | NC_000913 | 4577769 | 4580632 | 2864 | 32 [0] | [2] 3 | [mcrC]–[hsdS] | [mcrC],mcrB,mcrB,symE,symR,[hsdS] |
| * | * | ÷ | NC_000913 | 4580765 | 4581028 | 264 | 3 [2] | [0] 17 | hsdS | type I restriction enzyme EcoKI specificity subunit |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 566774 | 31 (0.910) | 13 (0.390) | 7/482 | 1.9 | 30.3% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 29 (0.860) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 780629 | 0 (0.000) | 17 (0.730) | 16/334 | 0.4 | 97.1% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 1 (0.040) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | 1207790 = | 13 (0.380) | 7 (0.220) | 7/454 | 1.8 | 46.4% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 4 (0.130) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 12 (0.350) | 8 (0.250) | 8/454 | 1.6 | 51.3% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 4 (0.130) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 18 (0.560) | 18/462 | 0.7 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 18 (0.560) | 17/462 | 0.7 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 16 (0.470) | 15/486 | 0.9 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 13 (0.380) | 12/486 | 1.2 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 32 (0.940) | 31/484 | 0.2 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4577768 | 0 (0.000) | coding (191/1047 nt) | mcrC | Type IV methyl‑directed restriction enzyme EcoKMcrBC subunit | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 17 (0.500) | 16/486 | 0.9 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4581029 = | 0 (0.000) | coding (434/1395 nt) | hsdS | type I restriction enzyme EcoKI specificity subunit | |||||
| * | ? | NC_000913 | = 4244072 | 1 (0.030) | 42 (1.230) | 40/486 | 0.1 | 98.8% | coding (1004/1545 nt) | malF | maltose ABC transporter membrane subunit MalF |
| ? | NC_000913 | 4249362 = | 0 (0.000) | intergenic (+51/‑192) | lamB/malM | maltose outer membrane channel/phage lambda receptor protein/maltose regulon periplasmic protein | |||||