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 | 45,885 | C→T | P27S (CCG→TCG) | yaaU → | putative transporter YaaU |
| RA | 160,864 | (C)6→7 | coding (623/705 nt) | sfsA ← | putative DNA‑binding transcriptional regulator of maltose metabolism |
| RA | 200,222 | T→G | N765K (AAT→AAG) | bamA → | outer membrane protein assembly factor BamA |
| RA | 217,690 | A→G | G362G (GGT→GGC) | proS ← | proline‑‑tRNA ligase |
| RA | 218,880 | C→T | intergenic (‑105/+7) | proS ← / ← trmO | proline‑‑tRNA ligase/tRNA m(6)t(6)A37 methyltransferase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 400,681 | A→G | G81G (GGT→GGC) | ddlA ← | D‑alanine‑‑D‑alanine ligase A |
| RA | 411,158 | A→G | intergenic (+106/+139) | mak → / ← araJ | manno(fructo)kinase/putative transport protein AraJ |
| RA | 453,507 | A→G | R13R (CGT→CGC) | ampG ← | muropeptide:H(+) symporter |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 562,673 | (C)6→7 | coding (338/984 nt) | sfmH → | putative fimbrial adhesin protein SfmH |
| RA | 580,905 | A→G | E24E (GAA→GAG) | nohD → | DLP12 prophage; putative DNA‑packaging protein NohD |
| RA | 726,736 | (T)7→8 | coding (301/2049 nt) | kdpB ← | K(+) transporting P‑type ATPase subunit KdpB |
| RA | 751,199 | T→C | N324S (AAC→AGC) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 794,981 | C→T | intergenic (+59/‑108) | acrZ → / → modA | multidrug efflux pump accessory protein AcrZ/molybdate ABC transporter periplasmic binding protein |
| RA | 813,844 | A→G | T107A (ACT→GCT) | uvrB → | excision nuclease subunit B |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 901,149 | C→T | G129E (GGA→GAA) | artM ← | L‑arginine ABC transporter membrane subunit ArtM |
| RA | 904,100 | A→G | V123A (GTG→GCG) | ybjP ← | DUF3828 domain‑containing lipoprotein YbjP |
| RA | 911,474 | T→C | K226R (AAA→AGA) | hcr ← | NADH oxidoreductase |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,096,310 | (A)6→5 | coding (468/987 nt) | ycdU → | uncharacterized protein YcdU |
| RA | 1,116,501 | A→G | L28L (TTA→CTA) | lpxL ← | lauroyl acyltransferase |
| 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 | 1,224,151 | A→G | intergenic (+244/+128) | ycgI → / ← minE | protein YcgI/Z‑ring positioning protein MinE |
| RA | 1,283,745 | C→T | P48S (CCG→TCG) | narH → | nitrate reductase A subunit beta |
| RA | 1,365,831 | C→T | A94A (GCC→GCT) | puuE → | 4‑aminobutyrate aminotransferase PuuE |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 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 | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,663,354 | A→G | H122R (CAC→CGC) | ynfG → | putative oxidoreductase YnfG |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,721,471 | (G)5→6 | coding (208/858 nt) | ydhJ → | putative membrane fusion protein YdhJ |
| RA | 1,731,408 | A→G | A774A (GCA→GCG) | lhr → | putative ATP‑dependent helicase Lhr |
| RA | 1,750,083 | G→A | A89V (GCC→GTC) | ydhU ← | putative cytochrome YdhU |
| RA | 1,784,424 | T→C | V483A (GTT→GCT) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,831,395 | G→A | G196G (GGC→GGT) | astC ← | succinylornithine transaminase |
| RA | 1,838,510 | G→A | V433V (GTG→GTA) | ynjC → | putative ABC transporter membrane subunit YnjC |
| 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 | 1,902,770 | G→A | M241I (ATG→ATA) | manX → | mannose‑specific PTS enzyme IIAB component |
| 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 | 2,005,893 | C→T | Q61* (CAG→TAG) | fliT → | flagellar biosynthesis protein FliT |
| RA | 2,024,659 | A→G | G55G (GGT→GGC) | dsrB ← | protein DsrB |
| RA | 2,132,499 | A→G | L19L (CTT→CTC) | wcaB ← | putative colanic acid biosynthesis acyl transferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,391,786 | G→A | P419L (CCG→CTG) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,496,460 | G→A | M272I (ATG→ATA) | lpxP → | palmitoleoyl acyltransferase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,621,670 | T→C | G158G (GGT→GGC) | purM → | phosphoribosylformylglycinamide cyclo‑ligase |
| RA | 2,695,585 | (G)7→8 | intergenic (‑42/‑216) | purL ← / → mltF | phosphoribosylformylglycinamide synthetase/membrane‑bound lytic murein transglycosylase F |
| RA | 2,765,794 | (C)7→8 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,784,617 | T→C | N132S (AAC→AGC) | ypjC ← | DUF5507 domain‑containing protein YpjC |
| RA | 2,806,297 | T→C | G96G (GGT→GGC) | proW → | glycine betaine ABC transporter membrane subunit ProW |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,905,219 | (C)6→5 | coding (200/672 nt) | queE ← | putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 2,917,723 | T→C | G889G (GGT→GGC) | barA → | sensory histidine kinase BarA |
| RA | 2,927,340 | G→A | D345N (GAT→AAT) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,928,276 | T→C | S16S (AGT→AGC) | sdaC → | serine:H(+) symporter SdaC |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,983,458 | G→A | P223S (CCG→TCG) | kduI ← | 5‑dehydro‑4‑deoxy‑D‑glucuronate isomerase |
| RA | 3,042,956 | A→G | F65L (TTC→CTC) | yqfA ← | hemolysin‑III family protein |
| RA | 3,060,796 | (A)5→4 | intergenic (+150/‑54) | argP → / → scpA | DNA‑binding transcriptional dual regulator ArgP/methylmalonyl‑CoA mutase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,143,408 | T→C | T253A (ACC→GCC) | hybB ← | hydrogenase 2 membrane subunit |
| RA | 3,219,963 | C→T | A157V (GCG→GTG) | patA → | putrescine aminotransferase |
| RA | 3,221,816 | T→C | G117G (GGT→GGC) | ebgR → | DNA‑binding transcriptional repressor EbgR |
| RA | 3,240,120 | (C)5→6 | coding (177/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,270,859 | T→C | V304V (GTA→GTG) | garK ← | glycerate 2‑kinase 1 |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,370,432 | +C | coding (605/690 nt) | nanE ← | putative N‑acetylmannosamine‑6‑phosphate epimerase |
| RA | 3,386,207 | G→T | intergenic (‑78/+14) | yhcO ← / ← aaeB | putative barnase inhibitor/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 | 3,390,319 | T→C | V267A (GTT→GCT) | aaeR → | LysR‑type transcriptional regulator AaeR |
| RA | 3,447,157 | T→C | E94E (GAA→GAG) | rplE ← | 50S ribosomal subunit protein L5 |
| RA | 3,462,381 | T→C | V13A (GTC→GCC) | gspJ → | Type II secretion system protein GspJ |
| RA | 3,522,907 | T→C | C13R (TGT→CGT) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,598,550 | A→G | intergenic (+183/+5) | panZ → / ← livJ | PanD maturation factor/branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein |
| RA | 3,692,872 | T→C | T789A (ACG→GCG) | bcsA ← | cellulose synthase catalytic subunit |
| RA | 3,719,916 | C→T | intergenic (+148/‑133) | yiaG → / → cspA | putative DNA‑binding transcriptional regulator YiaG/cold shock protein CspA |
| RA | 3,784,681 | T→C | N112S (AAC→AGC) | yibN ← | putative sulfurtransferase YibN |
| RA | 3,796,188 | (C)5→6 | coding (210/960 nt) | waaC → | ADP‑heptose:LPS heptosyltransferase 1 |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,859,745 | G→A | C124C (TGC→TGT) | yidK ← | putative transporter YidK |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,918,124 | T→C | T48A (ACC→GCC) | atpG ← | ATP synthase F1 complex subunit gamma |
| RA | 3,925,508 | +C | coding (126/1890 nt) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,932,121 | A→G | N269S (AAC→AGC) | kup → | K(+):H(+) symporter Kup |
| RA | 3,955,324 | (G)6→7 | coding (1847/1851 nt) | ilvD → | dihydroxy‑acid dehydratase |
| RA | 4,056,607 | C→T | intergenic (‑268/+18) | glnL ← / ← glnA | sensory histidine kinase NtrB/glutamine synthetase |
| RA | 4,129,619 | C→T | G316G (GGC→GGT) | metB → | O‑succinylhomoserine(thiol)‑lyase/O‑ succinylhomoserine lyase |
| RA | 4,192,296 | T→C | K114E (AAA→GAA) | thiG ← | 1‑deoxy‑D‑xylulose 5‑phosphate:thiol sulfurtransferase |
| RA | 4,247,335 | C→T | G184G (GGC→GGT) | malK → | maltose ABC transporter ATP binding subunit |
| RA | 4,280,799 | A→G | T274A (ACC→GCC) | yjcE → | putative transporter YjcE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,347,377 | T→C | intergenic (‑51/+27) | fumB ← / ← dcuB | fumarase B/anaerobic C4‑dicarboxylate transporter DcuB |
| RA | 4,399,779 | C→T | F176F (TTC→TTT) | miaA → | tRNA dimethylallyltransferase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,511,424 | A→G | Y12H (TAC→CAC) | fecE ← | ferric citrate ABC transporter ATP binding subunit |
| RA | 4,561,864 | (C)6→7 | coding (812/1179 nt) | yjiJ ← | putative transporter YjiJ |
| RA | 4,565,944 | C→T | intergenic (‑94/+22) | yjiM ← / ← yjiN | putative dehydratase subunit/DUF445 domain‑containing protein YjiN |
| RA | 4,581,809 | G→A | P414S (CCG→TCG) | hsdM ← | type I restriction enzyme EcoKI methyltransferase component |
| RA | 4,602,660 | T→C | T67A (ACA→GCA) | yjjP ← | putative succinate exporter YjjP |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423760–3424234 | 3424556–3424238 | 5–797 | 28 [26] | [26] 28 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375203 = | NA (NA) | 24 (0.330) | 16/216 | 2.9 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 1207790 = | 19 (0.200) | 101 (1.210) | 63/244 | 0.1 | 87.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 11 (0.130) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 19 (0.200) | 65 (0.780) | 41/244 | 0.7 | 82.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 11 (0.130) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 106 (1.150) | 63/268 | 0.2 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 147 (1.550) | 135 (1.440) | 71/274 | 0.1 | 64.6% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 126 (1.330) | 76/276 | 0.1 | 96.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||