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 | annotation | gene | description |
| RA | 95,385 | A→G | S246G (AGC→GGC) | murF → | D‑alanyl‑D‑alanine‑adding enzyme |
| RA | 164,554 | C→T | intergenic (+20/‑176) | hrpB → / → mrcB | putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| RA | 196,329 | T→C | V218A (GTC→GCC) | cdsA → | CDP‑diglyceride synthetase |
| RA | 244,404 | T→C | G26G (GGT→GGC) | yafJ → | putative amidotransferase |
| RA | 251,815 | G→A | R306R (CGG→CGA) | dinB → | DNA polymerase IV |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 305,321 | C→T | V499V (GTG→GTA) | ecpD ← | fimbrial adhesin EcpD |
| RA | 367,852 | (GC)6→5 | coding (568‑569/834 nt) | mhpR ← | DNA‑binding transcriptional activator MhpR |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 407,185 | T→C | intergenic (+15/‑243) | yaiA → / → aroM | protein YaiA/protein AroM |
| RA | 423,359 | A→G | Y281C (TAC→TGC) | malZ → | maltodextrin glucosidase |
| RA | 467,823 | (A)7→8 | coding (412/819 nt) | cof → | HMP‑PP phosphatase |
| RA | 468,892 | A→G | S8G (AGC→GGC) | mdlA → | ABC transporter family protein MdlA |
| RA | 495,135 | A→G | T6A (ACT→GCT) | htpG → | chaperone protein HtpG |
| RA | 496,463 | A→G | E448E (GAA→GAG) | htpG → | chaperone protein HtpG |
| RA | 498,344 | C→T | A97V (GCG→GTG) | hemH → | ferrochelatase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 697,363 | G→A | intergenic (‑230/+150) | metT ← / ← asnB | tRNA‑Met/asparagine synthetase B |
| RA | 721,955 | A→G | G820G (GGT→GGC) | kdpD ← | sensory histidine kinase KdpD |
| RA | 788,993 | T→C | V329V (GTA→GTG) | galK ← | galactokinase |
| RA | 868,422 | (C)8→7 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 910,772 | A→G | V93A (GTT→GCT) | poxB ← | pyruvate oxidase |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 974,611 | A→G | N98S (AAC→AGC) | mukF → | chromosome partitioning protein MukF |
| RA | 975,341 | A→G | E341E (GAA→GAG) | mukF → | chromosome partitioning protein MukF |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,011,868 | C→T | G635G (GGC→GGT) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,014,720 | A→G | M488V (ATG→GTG) | pqiB → | intermembrane transport protein PqiB |
| RA | 1,097,580 | (G)7→8 | noncoding (73/88 nt) | serX ← | tRNA‑Ser |
| RA | 1,127,049 | A→G | T82A (ACG→GCG) | yceM → | putative oxidoreductase YceM |
| RA | 1,134,936 | A→G | T70A (ACG→GCG) | flgG → | flagellar basal‑body rod protein FlgG |
| RA | 1,140,782 | A→G | L250L (TTA→TTG) | flgL → | flagellar hook‑filament junction protein 2 |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,242,080 | T→C | intergenic (‑9/+86) | cvrA ← / ← ldcA | putative K(+):H(+) antiporter/murein L,D‑carboxypeptidase |
| RA | 1,292,624 | A→G | V100A (GTT→GCT) | hns ← | DNA‑binding transcriptional dual regulator H‑NS |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,335,827 | A→G | intergenic (+160/‑4) | ymiC → / → acnA | protein YmiC/aconitate hydratase 1 |
| RA | 1,340,358 | A→G | Y39C (TAC→TGC) | lapA → | lipopolysaccharide assembly protein A |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,387,478 | A→G | R253R (AGA→AGG) | tyrR → | DNA‑binding transcriptional dual regulator TyrR |
| RA | 1,412,060 | A→G | G392G (GGT→GGC) | intR ← | Rac prophage; putative integrase |
| RA | 1,412,373 | T→C | Y288C (TAC→TGC) | intR ← | Rac prophage; putative integrase |
| RA | 1,425,452 | A→G | S26G (AGT→GGT) | ynaK → | Rac prophage; ParB‑like nuclease domain‑containing protein YnaK |
| RA | 1,440,941 | (A)7→8 | intergenic (‑157/‑117) | ydbK ← / → ydbJ | putative pyruvate‑flavodoxin oxidoreductase/DUF333 domain‑containing protein YdbJ |
| RA | 1,441,545 | A→G | C67R (TGT→CGT) | hslJ ← | lipoprotein implicated in Novobiocin resistance |
| RA | 1,467,427 | A→G | pseudogene (2036/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,479,687 | (G)6→7 | coding (550/1758 nt) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,485,103 | (G)5→4 | coding (2043/3903 nt) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,490,865 | T→C | intergenic (‑152/‑37) | gapC ← / → cybB | glyceraldehyde‑3‑phosphate dehydrogenase/cytochrome b561 |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| RA | 1,793,727 | G→A | A128V (GCC→GTC) | btuE ← | thioredoxin/glutathione peroxidase |
| RA | 1,848,406 | T→C | T91A (ACG→GCG) | ydjA ← | putative oxidoreductase |
| RA | 1,865,044 | T→C | Q198R (CAG→CGG) | yeaE ← | methylglyoxal reductase YeaE |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,917,898 | A→G | N130S (AAC→AGC) | yebT → | intermembrane transport protein YebT |
| RA | 1,977,972 | T→C | T76A (ACT→GCT) | flhD ← | DNA‑binding transcriptional dual regulator FlhD |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 1,997,140 | (C)5→6 | coding (675/753 nt) | tcyN ← | cystine ABC transporter ATP binding subunit |
| RA | 2,005,518 | T→C | S72S (AGT→AGC) | fliS → | flagellar biosynthesis protein FliS |
| RA | 2,168,566 | T→C | intergenic (‑260/‑146) | yegR ← / → yegS | uncharacterized protein YegR/lipid kinase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,326,014 | G→A | G420D (GGC→GAC) | atoE → | short chain fatty acid transporter |
| RA | 2,369,659 | C→T | R541C (CGC→TGC) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,370,767 | A→G | K250K (AAA→AAG) | arnD → | putative 4‑deoxy‑4‑formamido‑L‑arabinose‑phosphoundecaprenol deformylase ArnD |
| RA | 2,391,841 | T→C | T401A (ACC→GCC) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,447,083 | T→C | T131A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,476,771 | T→C | T287A (ACA→GCA) | dsdC ← | DNA‑binding transcriptional dual regulator DsdC |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,537,664 | (T)6→7 | coding (323/375 nt) | yfeK → | protein YfeK |
| RA | 2,558,827 | T→C | intergenic (‑148/‑31) | eutB ← / → intZ | ethanolamine ammonia‑lyase subunit alpha/CPZ‑55 prophage; putative phage integrase IntZ |
| RA | 2,611,639 | T→C | D61D (GAT→GAC) | hyfJ → | putative hydrogenase 4 assembly protein |
| RA | 2,656,816 | G→A | R90C (CGC→TGC) | fdx ← | reduced ferredoxin |
| RA | 2,685,709 | G→A | intergenic (‑202/‑126) | glyA ← / → hmp | serine hydroxymethyltransferase/nitric oxide dioxygenase |
| RA | 2,703,236 | G→A | H51Y (CAT→TAT) | era ← | 30S ribosomal subunit maturation GTPase Era |
| RA | 2,765,774 | (C)5→6 | coding (3/264 nt) | yfjM ← | CP4‑57 prophage; protein YfjM |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,848,370 | T→C | H291R (CAC→CGC) | hycC ← | formate hydrogenlyase subunit HycC |
| RA | 2,855,075 | G→A | Q246Q (CAG→CAA) | fhlA → | DNA‑binding transcriptional activator FhlA |
| RA | 2,856,646 | T→C | K54R (AAA→AGA) | ygbA ← | protein YgbA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,881,944 | G→A | H67Y (CAT→TAT) | casC ← | type I‑E CRISPR system Cascade subunit CasC |
| RA | 2,936,765 | T→C | G394G (GGT→GGC) | fucI → | L‑fucose isomerase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,992,892 | T→C | Y267H (TAC→CAC) | ygeH → | putative transcriptional regulator YgeH |
| RA | 3,000,854 | A→G | V170V (GTA→GTG) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,027,312 | A→G | A64A (GCA→GCG) | ghxQ → | guanine/hypoxanthine transporter GhxQ |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,080,867 | T→C | T257A (ACC→GCC) | tktA ← | transketolase 1 |
| RA | 3,134,525 | A→G | N132S (AAC→AGC) | yghT → | putative ATP‑binding protein YghT |
| RA | 3,151,963 | T→C | T8A (ACG→GCG) | exbB ← | Ton complex subunit ExbB |
| RA | 3,157,770 | A→G | T41A (ACT→GCT) | yqhG → | DUF3828 domain‑containing protein YqhG |
| RA | 3,173,650 | T→C | T583A (ACT→GCT) | parE ← | DNA topoisomerase IV subunit B |
| RA | 3,194,986 | A→G | intergenic (‑121/+111) | sibD ← / ← sibE | small RNA SibD/small RNA SibE |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,432,994 | (C)6→7 | coding (567/1125 nt) | smf ← | protein Smf |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,636,286 | (C)6→7 | coding (1125/1203 nt) | yhiN ← | putative oxidoreductase YhiN |
| RA | 3,639,576 | (A)6→5 | coding (145/336 nt) | uspB ← | putative universal stress (ethanol tolerance) protein B |
| RA | 3,649,857 | T→C | V308A (GTA→GCA) | arsB → | arsenite/antimonite:H(+) antiporter |
| RA | 3,668,544 | (C)6→7 | coding (645/1398 nt) | ccp ← | cytochrome c peroxidase |
| RA | 3,683,627 | T→C | intergenic (‑180/+3) | dctA ← / ← pdeK | C4 dicarboxylate/orotate:H(+) symporter/putative c‑di‑GMP phosphodiesterase PdeK |
| RA | 3,728,118 | (C)8→9 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,935,010 | G→A | M411I (ATG→ATA) | rbsA → | ribose ABC transporter ATP binding subunit |
| JC JC | 4,063,721 | IS1 (–) +9 bp | coding (567‑575/693 nt) | ompL ← | putative outer membrane porin L |
| RA | 4,229,967 | G→A | P59L (CCG→CTG) | pepE ← | peptidase E |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,302,258 | (T)5→4 | coding (821/2052 nt) | mdtO ← | putative multidrug efflux pump subunit MdtO |
| RA | 4,398,693 | C→T | L428F (CTT→TTT) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,400,845 | A→G | V58V (GTA→GTG) | hflX → | ribosome rescue factor HflX |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,518,178 | G→A | H20Y (CAT→TAT) | fecI ← | RNA polymerase sigma factor FecI |
| RA | 4,546,701 | C→T | Q536* (CAA→TAA) | fimD → | type I fimbriae usher protein |
| RA | 4,606,331 | A→G | noncoding (71/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,630,685 | A→G | intergenic (‑163/‑48) | ettA ← / → slt | energy‑dependent translational throttle protein EttA/soluble lytic murein transglycosylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423772–3424234 | 3424526–3424239 | 6–755 | 17 [16] | [16] 19 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 16 (0.220) | 94 (1.460) | 56/244 | 0.1 | 90.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 5 (0.080) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.220) | 42 (0.650) | 29/244 | 0.9 | 81.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 5 (0.080) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1979486 = | 44 (0.610) | 28 (0.390) | 15/276 | 2.8 | 38.9% | intergenic (‑271/‑267) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1979489 | 43 (0.590) | 25 (0.340) | 15/276 | 2.8 | 36.8% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 3363001 = | 128 (1.760) | 148 (2.050) | 79/274 | 0.0 | 69.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.010) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 104 (1.430) | 67/276 | 0.0 | 96.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||