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 | 7,354 | C→T | R202R (CGG→CGA) | yaaJ ← | putative transporter YaaJ |
| RA | 45,901 | A→G | Y32C (TAT→TGT) | yaaU → | putative transporter YaaU |
| RA | 88,245 | A→G | N73S (AAC→AGC) | cra → | DNA‑binding transcriptional dual regulator Cra |
| RA | 125,804 | T→C | V37A (GTA→GCA) | aceF → | pyruvate dehydrogenase, E2 subunit |
| RA | 141,576 | Δ1 bp | coding (146/537 nt) | hpt → | hypoxanthine phosphoribosyltransferase |
| RA | 189,420 | T→C | E29E (GAA→GAG) | map ← | methionine aminopeptidase |
| RA | 191,783 | T→C | intergenic (+75/‑72) | tsf → / → pyrH | protein chain elongation factor EF‑Ts/UMP kinase |
| RA | 218,835 | (A)8→7 | intergenic (‑60/+52) | proS ← / ← trmO | proline‑‑tRNA ligase/tRNA m(6)t(6)A37 methyltransferase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 261,052 | A→G | D222G (GAC→GGC) | proB → | glutamate 5‑kinase |
| RA | 317,091 | A→G | pseudogene (46/687 nt) | ykgA ← | putative DNA‑binding transcriptional regulator YkgA |
| JC JC | 317,587 | IS5 (+) +4 bp | intergenic (‑451/+136) | ykgA ← / ← rclC | putative DNA‑binding transcriptional regulator YkgA/reactive chlorine species resistance protein C |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 381,052 | A→G | pseudogene (209/417 nt) | yaiX ← | putative acyltransferase, N‑terminal fragment |
| RA | 423,296 | A→G | D260G (GAC→GGC) | malZ → | maltodextrin glucosidase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| MC JC | 545,679 | (TCA)4→3 | coding (683‑685/1050 nt) | allD ← | ureidoglycolate dehydrogenase |
| RA | 560,965 | C→T | G423G (GGC→GGT) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 564,815 | T→C | *388* (TAA→TAG) | intD ← | DLP12 prophage; putative integrase |
| RA | 580,775 | A→G | intergenic (‑330/‑59) | ylcI ← / → nohD | DLP12 prophage; DUF3950 domain‑containing protein YlcI/DLP12 prophage; putative DNA‑packaging protein NohD |
| RA | 590,002 | A→G | V318A (GTT→GCT) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 607,587 | (A)7→8 | intergenic (‑204/‑147) | ybdK ← / → sokE | carboxylate‑amine ligase/small RNA SokE |
| RA | 629,623 | T→C | G108G (GGT→GGC) | entH → | proofreading thioesterase in enterobactin biosynthesis |
| RA | 668,204 | T→C | N5S (AAC→AGC) | mrdA ← | peptidoglycan DD‑transpeptidase MrdA |
| RA | 710,846 | A→G | intergenic (‑121/+89) | uof ← / ← fldA | RyhB‑regulated fur leader peptide/flavodoxin 1 |
| RA | 716,455 | A→G | pseudogene (143/651 nt) | ybfG ← | PF10964 domain‑containing protein YbfG |
| RA | 794,261 | A→G | R128R (CGT→CGC) | modE ← | DNA‑binding transcriptional dual regulator ModE |
| RA | 868,422 | (C)8→9 | 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 | 902,160 | A→G | F31L (TTC→CTC) | artQ ← | L‑arginine ABC transporter membrane subunit ArtQ |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 986,775 | C→T | E70K (GAA→AAA) | ompF ← | outer membrane porin F |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,097,580 | (G)7→8 | noncoding (73/88 nt) | serX ← | tRNA‑Ser |
| RA | 1,097,592 | (C)5→6 | noncoding (61/88 nt) | serX ← | tRNA‑Ser |
| RA | 1,141,297 | C→T | R1024H (CGT→CAT) | rne ← | ribonuclease E |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,147,109 | T→C | Y106H (TAT→CAT) | yceD → | DUF177 domain‑containing protein YceD |
| RA | 1,159,499 | A→G | Y685H (TAC→CAC) | fhuE ← | ferric coprogen/ferric rhodotorulic acid outer membrane transporter |
| JC | 1,198,505 | (AATGATGA)6→7 | intergenic (‑268/‑190) | ymfE ← / → lit | e14 prophage; uncharacterized protein YmfE/e14 prophage; cell death peptidase Lit |
| RA | 1,212,088 | (C)8→7 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,217,888 | A→G | G187G (GGA→GGG) | pdeG → | putative c‑di‑GMP phosphodiesterase PdeG |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,231,001 | A→G | T79A (ACC→GCC) | umuD → | DNA polymerase V protein UmuD |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,351,001 | A→G | G13G (GGT→GGC) | fabI ← | enoyl‑[acyl‑carrier‑protein] reductase |
| RA | 1,371,613 | G→A | R466R (AGG→AGA) | ycjM → | glucosylglycerate phosphorylase |
| RA | 1,399,978 | T→C | T87A (ACG→GCG) | ogt ← | methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| RA | 1,409,250 | (T)8→7 | intergenic (+3/‑58) | fnrS → / → ynaL | small regulatory RNA FnrS/protein YnaL |
| RA | 1,420,793 | (G)6→5 | coding (110/423 nt) | ydaT → | Rac prophage; protein YdaT |
| RA | 1,496,794 | C→T | intergenic (+163/‑62) | ydcJ → / → opgD | DUF1338 domain‑containing protein YdcJ/glucan biosynthesis protein D |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,597,313 | (C)7→8 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,605,789 | A→G | T247A (ACG→GCG) | lsrB → | Autoinducer‑2 ABC transporter periplasmic binding protein |
| 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 | 1,690,803 | A→G | T318A (ACT→GCT) | ydgA → | conserved protein YdgA |
| RA | 1,793,592 | A→G | V173A (GTG→GCG) | btuE ← | thioredoxin/glutathione peroxidase |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,877,653 | T→C | intergenic (‑121/‑62) | yoaF ← / → dgcP | DUF333 domain‑containing lipoprotein YoaF/diguanylate cyclase DgcP |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,925,458 | G→A | A7T (GCA→ACA) | yobB → | putative carbon‑nitrogen hydrolase family protein YobB |
| 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 | 2,098,169 | C→T | A45T (GCT→ACT) | wzzB ← | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,300,287 | C→T | V823I (GTC→ATC) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,301,322 | T→C | T478A (ACC→GCC) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,342,036 | A→G | F712L (TTC→CTC) | yfaL ← | putative autotransporter adhesin YfaL |
| RA | 2,367,339 | A→G | H90R (CAC→CGC) | arnC → | undecaprenyl‑phosphate 4‑deoxy‑4‑formamido‑L‑arabinose transferase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,838,610 | T→C | N219D (AAC→GAC) | ascG ← | DNA‑binding transcriptional repressor AscG |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,912,216 | T→C | N479S (AAC→AGC) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,935,179 | T→C | G315G (GGT→GGC) | fucP → | L‑fucose:H(+) symporter |
| RA | 2,941,028 | Δ1 bp | coding (216/1101 nt) | rlmM ← | 23S rRNA 2'‑O‑ribose C2498 methyltransferase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,016,853 | T→C | V265A (GTT→GCT) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,024,721 | T→C | V124A (GTC→GCC) | xanQ → | xanthine:H(+) symporter XanQ |
| RA | 3,054,695 | T→C | D49G (GAC→GGC) | pepP ← | proline aminopeptidase P II |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,089,687 | A→G | intergenic (+9/‑68) | galP → / → yggI | galactose:H(+) symporter/conserved protein YggI |
| RA | 3,115,428 | T→C | T1229A (ACC→GCC) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,162,483 | T→C | T63A (ACA→GCA) | ftsP ← | cell division protein required during stress conditions |
| RA | 3,201,283 | G→A | R26H (CGC→CAC) | ygiM → | putative signal transduction protein (SH3 domain) |
| RA | 3,222,943 | T→C | V104A (GTC→GCC) | ebgA → | evolved beta‑D‑galactosidase subunit alpha |
| RA | 3,296,535 | A→G | T43A (ACC→GCC) | yraP → | divisome‑associated lipoprotein YraP |
| RA | 3,316,792 | G→A | I245I (ATC→ATT) | nusA ← | transcription termination/antitermination protein NusA |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,379,266 | (C)7→8 | coding (732/1128 nt) | zapE ← | cell division factor ZapE with ATPase activity |
| RA | 3,387,282 | T→C | T303A (ACG→GCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,596,819 | G→A | P248S (CCG→TCG) | livK ← | L‑leucine/L‑phenylalanine ABC transporter periplasmic binding protein |
| RA | 3,619,272 | T→C | R27R (CGT→CGC) | rhsB → | rhs element protein RhsB |
| RA | 3,660,262 | T→C | V344A (GTC→GCC) | mdtE → | multidrug efflux pump membrane fusion protein MdtE |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,828,111 | T→C | K185K (AAA→AAG) | gltS ← | glutamate:sodium symporter |
| RA | 3,847,243 | T→C | intergenic (‑76/+62) | uhpT ← / ← uhpC | hexose‑6‑phosphate:phosphate antiporter/inner membrane protein sensing glucose‑6‑phosphate |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,873,782 | G→A | G231G (GGC→GGT) | dgoK ← | 2‑dehydro‑3‑deoxygalactonokinase |
| JC | 3,931,183 | (G)7→10 | intergenic (‑90/‑133) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 3,966,740 | A→G | E108E (GAA→GAG) | rho → | transcription termination factor Rho |
| RA | 3,988,081 | T→C | D329G (GAC→GGC) | hemX ← | PF04375 family protein HemX |
| RA | 4,046,213 | C→T | Q130Q (CAG→CAA) | yihG ← | putative acyltransferase YihG |
| RA | 4,293,106 | (G)7→8 | coding (1595/1659 nt) | nrfE → | putative cytochrome c‑type biogenesis protein NrfE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,313,658 | C→T | N103N (AAC→AAT) | rpiB → | allose‑6‑phosphate isomerase/ribose‑5‑phosphate isomerase B |
| RA | 4,354,241 | A→G | G159G (GGT→GGC) | lysU ← | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| RA | 4,445,428 | A→G | Q439Q (CAA→CAG) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,490,576 | A→G | G188G (GGT→GGC) | idnR ← | DNA‑binding transcriptional dual regulator IdnR |
| RA | 4,541,444 | A→G | D163G (GAT→GGT) | fimB → | regulator for fimA |
| RA | 4,575,592 | C→T | pseudogene (1458/2721 nt) | yjiV → | putative uncharacterized protein YjiV |
| RA | 4,622,228 | A→G | T154A (ACT→GCT) | yjjJ → | toxin YjjJ |
| RA | 4,634,014 | A→G | D73G (GAC→GGC) | ytjC → | putative phosphatase |
| RA | 4,636,877 | A→G | D61G (GAC→GGC) | creC → | sensory histidine kinase CreC |
| RA | 4,637,601 | G→A | A302A (GCG→GCA) | creC → | sensory histidine kinase CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2520974 | 2521055 | 82 | 14 [13] | [13] 14 | [valU]–[valX] | [valU],[valX] |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424528–3424238 | 5–759 | 15 [11] | [11] 15 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 224435 | NA (NA) | 70 (1.130) +GGG |
40/258 | 0.3 | NA | noncoding (665/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | 224436 = | NA (NA) | noncoding (666/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 1207790 = | 68 (1.070) | 19 (0.340) | 15/244 | 2.1 | 27.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 40 (0.710) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 63 (0.990) | 86 (1.360) | 45/274 | 0.2 | 72.7% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 94 (1.480) | 61/276 | 0.0 | 99.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||