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 | 47,926 | A→G | E53G (GAA→GGA) | kefC → | K(+) : H(+) antiporter KefC |
| RA | 119,401 | G→T | G41W (GGG→TGG) | ampE → | protein AmpE |
| RA | 179,045 | G→T | Q37K (CAA→AAA) | mtn ← | 5'‑methylthioadenosine/S‑adenosylhomocysteine nucleosidase |
| RA | 179,661 | C→A | P142Q (CCG→CAG) | dgt → | dGTP triphosphohydrolase |
| RA | 195,050 | G→T | V50F (GTC→TTC) | ispU → | undecaprenyl diphosphate synthase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 260,845 | C→A | S153Y (TCT→TAT) | proB → | glutamate 5‑kinase |
| RA | 282,103 | C→T | intergenic (‑120/‑175) | yagA ← / → yagE | CP4‑6 prophage; integrase core domain‑containing protein YagA/CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase |
| RA | 317,190 | C→G | intergenic (‑54/+536) | ykgA ← / ← rclC | putative DNA‑binding transcriptional regulator YkgA/reactive chlorine species resistance protein C |
| RA | 318,995 | G→A | P336L (CCG→CTG) | rclA ← | putative pyridine nucleotide‑disulfide oxidoreductase RclA |
| RA | 370,197 | C→A | G529G (GGC→GGA) | mhpA → | putative 3‑(3‑hydroxyphenyl)propanoate/3‑hydroxycinnamate hydroxylase |
| RA | 390,305 | C→A | pseudogene (55/1458 nt) | yaiT → | putative autotransporter YaiT |
| RA | 408,727 | C→A | pseudogene (119/342 nt) | ykiA → | DUF2773 domain‑containing protein YkiA |
| RA | 485,151 | C→A | V157L (GTA→TTA) | acrA ← | multidrug efflux pump membrane fusion lipoprotein AcrA |
| RA | 500,023 | A→T | intergenic (‑50/‑102) | aes ← / → gsk | acetylesterase/inosine/guanosine kinase |
| RA | 525,916 | C→A | R886R (CGG→AGG) | rhsD → | protein RhsD |
| RA | 528,727 | C→A | pseudogene (88/491 nt) | ybbD → | putative uncharacterized protein YbbD |
| RA | 631,430 | G→T | D513Y (GAT→TAT) | cstA → | carbon starvation protein A |
| RA | 643,088 | C→A | T334N (ACC→AAC) | ybdR → | putative Zn(2(+))‑dependent alcohol dehydrogenase YbdR |
| RA | 845,933 | C→A | K177N (AAG→AAT) | glnQ ← | L‑glutamine ABC transporter ATP binding subunit |
| RA | 887,760 | C→T | A113V (GCT→GTT) | rcdA → | DNA‑binding transcriptional regulator RcdA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 903,996 | G→T | H158N (CAT→AAT) | ybjP ← | DUF3828 domain‑containing lipoprotein YbjP |
| RA | 914,655 | C→A | S68I (AGT→ATT) | lysO ← | L‑lysine exporter |
| RA | 997,277 | G→T | A79D (GCC→GAC) | ssuE ← | NADPH‑dependent FMN reductase |
| RA | 999,300 | G→T | A29S (GCA→TCA) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,011,738 | C→A | A592E (GCG→GAG) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,079,316 | C→A | S4R (AGC→AGA) | putP → | proline:Na(+) symporter |
| RA | 1,114,221 | G→T | intergenic (‑40/+43) | msyB ← / ← mdtG | acidic protein that suppresses heat sensitivity of a secY mutant/efflux pump MdtG |
| RA | 1,152,670 | C→G | Y244* (TAC→TAG) | fabF → | beta‑ketoacyl‑[acyl carrier protein] synthase II |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,224,719 | G→T | Q215K (CAA→AAA) | minD ← | Z‑ring positioning protein MinD |
| RA | 1,324,419 | C→A | P108T (CCA→ACA) | yciO → | putative RNA‑binding protein YciO |
| RA | 1,398,477 | G→A | T49I (ACC→ATC) | uspE ← | universal stress protein with a role cellular motility |
| RA | 1,479,559 | C→A | A141D (GCC→GAC) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,484,100 | C→A | A347E (GCG→GAG) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,612,318 | G→T | S3Y (TCT→TAT) | yneG ← | conserved protein YneG |
| RA | 1,653,800 | G→T | S39* (TCA→TAA) | rspB ← | putative zinc‑binding dehydrogenase RspB |
| RA | 1,669,517 | G→T | R26S (CGC→AGC) | ynfL ← | putative DNA‑binding transcriptional regulator |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,743,649 | C→A | L65M (CTG→ATG) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,866,722 | C→A | intergenic (‑250/‑186) | mipA ← / → yeaG | scaffolding protein that interacts with murein polymerase and murein hydrolase/protein kinase YeaG |
| RA | 1,878,976 | G→T | intergenic (+28/+31) | yoaJ → / ← yeaQ | uncharacterized protein YoaJ/PF04226 family protein YeaQ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,885,032 | C→T | A123V (GCC→GTC) | yeaW → | carnitine monooxygenase subunit YeaW |
| RA | 1,942,110 | G→T | I158I (ATC→ATA) | znuA ← | Zn(2(+)) ABC transporter periplasmic binding protein |
| RA | 1,955,731 | G→T | A426E (GCG→GAG) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,029,529 | G→T | intergenic (‑163/‑10) | yedI ← / → yedA | conserved inner membrane protein YedI/putative transporter YedA |
| RA | 2,158,712 | G→T | Q109H (CAG→CAT) | mdtC → | multidrug efflux pump RND permease subunit MdtC |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,258,528 | C→A | A257S (GCC→TCC) | psuK ← | putative pseudouridine kinase |
| RA | 2,295,414 | G→T | A58E (GCG→GAG) | ccmD ← | heme trafficking system membrane protein CcmD |
| RA | 2,318,597 | C→A | S427I (AGC→ATC) | rcsC ← | sensory histidine kinase RcsC |
| RA | 2,370,399 | G→T | D128Y (GAT→TAT) | arnD → | putative 4‑deoxy‑4‑formamido‑L‑arabinose‑phosphoundecaprenol deformylase ArnD |
| RA | 2,418,808 | G→T | V123V (GTC→GTA) | yfcD ← | putative Nudix hydrolase |
| RA | 2,443,487 | C→G | P575R (CCA→CGA) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,445,170 | C→A | G131C (GGT→TGT) | yfcA ← | conserved inner membrane protein YfcA |
| RA | 2,461,237 | C→A | intergenic (‑303/‑69) | yfcZ ← / → fadL | DUF406 domain‑containing protein YfcZ/long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor |
| RA | 2,597,788 | A→T | intergenic (‑170/+43) | purC ← / ← bamC | phosphoribosylaminoimidazole‑succinocarboxamide synthase/outer membrane protein assembly factor BamC |
| RA | 2,606,469 | C→A | L70M (CTG→ATG) | hyfE → | hydrogenase 4 component E |
| RA | 2,607,682 | C→A | L256M (CTG→ATG) | hyfF → | hydrogenase 4 component F |
| RA | 2,666,255 | G→T | S274I (AGT→ATT) | csiE → | stationary phase inducible protein CsiE |
| RA | 2,724,344 | C→A | L73I (CTT→ATT) | yfiM → | protein YfiM |
| RA | 2,731,201 | T→G | intergenic (‑44/+399) | rrsG ← / ← clpB | 16S ribosomal RNA/ClpB chaperone |
| RA | 2,834,711 | A→C | D267A (GAT→GCT) | norW → | NADH:flavorubredoxin reductase |
| RA | 2,866,723 | G→T | R277R (CGA→AGA) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,892,278 | C→A | P22Q (CCG→CAG) | queD → | 6‑carboxy‑5,6,7,8‑tetrahydropterin synthase |
| RA | 2,901,145 | G→T | G185V (GGG→GTG) | yqcE → | putative transport protein YqcE |
| RA | 2,939,128 | C→T | L81F (CTC→TTC) | fucU → | L‑fucose mutarotase |
| RA | 3,315,121 | G→A | G298G (GGC→GGT) | infB ← | translation initiation factor IF‑2 |
| RA | 3,345,871 | C→A | T385T (ACC→ACA) | rpoN → | RNA polymerase, sigma 54 (sigma N) factor |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,379,824 | C→A | K58N (AAG→AAT) | zapE ← | cell division factor ZapE with ATPase activity |
| RA | 3,449,112 | G→T | L20M (CTG→ATG) | rplP ← | 50S ribosomal subunit protein L16 |
| RA | 3,450,977 | G→T | L130M (CTG→ATG) | rplB ← | 50S ribosomal subunit protein L2 |
| RA | 3,514,325 | G→T | A22D (GCT→GAT) | gph ← | phosphoglycolate phosphatase |
| RA | 3,542,452 | G→T | G682G (GGG→GGT) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,546,487 | C→T | intergenic (+288/‑72) | nfuA → / → gntT | iron‑sulfur cluster carrier protein NfuA/high‑affinity gluconate transporter |
| RA | 3,552,992 | C→T | intergenic (‑519/‑93) | malP ← / → malT | maltodextrin phosphorylase/DNA‑binding transcriptional activator MalT |
| RA | 3,553,699 | C→A | A205A (GCC→GCA) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,567,589 | C→A | A149S (GCG→TCG) | glgA ← | glycogen synthase |
| RA | 3,582,760 | G→T | A300S (GCA→TCA) | yhhZ → | putative endonuclease YhhZ |
| RA | 3,654,208 | A→G | K83R (AAG→AGG) | slp → | starvation lipoprotein |
| RA | 3,666,975 | G→T | T202T (ACC→ACA) | gadA ← | glutamate decarboxylase A |
| RA | 3,676,983 | C→A | A456A (GCG→GCT) | yhjG ← | AsmA family protein YhjG |
| RA | 3,790,071 | C→A | S4I (AGC→ATC) | waaH ← | UDP‑glucuronate:LPS(HepIII) glycosyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,924,436 | C→A | G400C (GGT→TGT) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,946,200 | A→T | noncoding (2497/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 4,001,946 | C→A | A174E (GCG→GAG) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,042,058 | G→T | intergenic (‑59/‑11) | mobA ← / → yihD | molybdenum cofactor guanylyltransferase/conserved protein YihD |
| RA | 4,065,475 | C→G | A98P (GCG→CCG) | yihO ← | putative sulfoquinovose transporter |
| RA | 4,090,951 | C→A | A472A (GCG→GCT) | frvB ← | putative PTS enzyme IIBC component FrvB |
| RA | 4,110,043 | C→A | V38V (GTC→GTA) | cdh → | CDP‑diacylglycerol diphosphatase |
| RA | 4,116,835 | C→A | G130C (GGT→TGT) | glpK ← | glycerol kinase |
| RA | 4,117,187 | C→A | Q12H (CAG→CAT) | glpK ← | glycerol kinase |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,275,832 | C→A | A121D (GCC→GAC) | pdeC → | c‑di‑GMP phosphodiesterase PdeC |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,364,950 | G→A | V31V (GTC→GTT) | dsbD ← | protein disulfide oxidoreductase ‑ DsbDreduced |
| RA | 4,426,475 | G→C | R123P (CGT→CCT) | rplI → | 50S ribosomal subunit protein L9 |
| RA | 4,433,658 | T→G | K123Q (AAA→CAA) | qorB ← | NAD(P)H:quinone oxidoreductase |
| RA | 4,450,011 | C→A | S17Y (TCT→TAT) | ytfQ → | galactofuranose ABC transporter periplasmic binding protein |
| RA | 4,481,631 | C→G | R736P (CGC→CCC) | valS ← | valine‑‑tRNA ligase |
| RA | 4,495,662 | A→T | I183N (ATC→AAC) | ahr ← | aldehyde reductase, NADPH‑dependent |
| RA | 4,529,294 | G→T | A317D (GCC→GAC) | sgcC ← | putative PTS enzyme IIC component SgcC |
| RA | 4,546,712 | C→A | R539R (CGC→CGA) | fimD → | type I fimbriae usher protein |
| RA | 4,549,284 | C→A | N159K (AAC→AAA) | fimH → | type 1 fimbriae D‑mannose specific adhesin |
| RA | 4,588,037 | G→T | Q277K (CAG→AAG) | yjiA ← | P‑loop guanosine triphosphatase |
| RA | 4,619,285 | Δ1 bp | coding (1057/1323 nt) | deoA → | thymidine phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196274 | 1211429 | 15156 | 22 [21] | [20] 22 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3102973 | 3104051 | 1079 | 22 [21] | [18] 22 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423756–3424525 | 3424525 | 1–770 | 22 [21] | [16] 22 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 109 (1.260) | 62/270 | 0.1 | 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 = | 142 (1.590) | 138 (1.560) | 70/276 | 0.1 | 65.7% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 80 (0.900) | 55/278 | 0.2 | 94.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||