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 | 10,265 | A→G | L77P (CTG→CCG) | satP ← | acetate/succinate:H(+) symporter |
| RA | 19,445 | C→T | P244L (CCA→CTA) | nhaR → | DNA‑binding transcriptional activator NhaR |
| RA | 34,120 | (T)9→8 | intergenic (+82/‑180) | carB → / → caiF | carbamoyl phosphate synthetase subunit beta/DNA‑binding transcriptional activator CaiF |
| RA | 116,675 | T→C | N142S (AAC→AGC) | hofB ← | T2SSE family protein |
| RA | 130,483 | C→T | A260T (GCC→ACC) | yacH ← | DUF3300 domain‑containing protein YacH |
| RA | 133,045 | C→T | G477G (GGC→GGT) | acnB → | hypothetical protein |
| RA | 141,718 | G→A | L96L (CTG→CTA) | hpt → | hypoxanthine phosphoribosyltransferase |
| RA | 149,066 | A→G | V179A (GTG→GCG) | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| RA | 214,389 | T→C | P33P (CCT→CCC) | yaeQ → | uncharacterized protein YaeQ |
| RA | 245,217 | G→A | Q197* (CAA→TAA) | yafK ← | L,D‑transpeptidase domain‑containing protein YafK |
| RA | 247,005 | A→G | R98R (AGA→AGG) | yafL → | NlpC/P60 family protein YafL |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 313,451 | T→C | intergenic (‑209/+265) | ykgR ← / ← ykgP | putative membrane protein YkgR/putative oxidoreductase |
| RA | 340,974 | C→T | F270F (TTC→TTT) | yahI → | carbamate kinase‑like protein YahI |
| RA | 370,874 | A→G | S200G (AGC→GGC) ‡ | mhpB → | 3‑carboxyethylcatechol 2,3‑dioxygenase |
| RA | 411,056 | (A)6→7 | intergenic (+4/+241) | mak → / ← araJ | manno(fructo)kinase/putative transport protein AraJ |
| RA | 435,252 | A→G | D39G (GAT→GGT) | nusB → | transcription antitermination protein NusB |
| RA | 441,683 | C→T | R45R (CGC→CGT) | thiI → | tRNA uridine 4‑sulfurtransferase |
| RA | 513,145 | (C)6→5 | coding (570/1293 nt) | ybaT → | putative transporter YbaT |
| RA | 525,211 | A→G | T651A (ACC→GCC) | rhsD → | protein RhsD |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 597,488 | (A)7→8 | coding (10/1224 nt) | cusB → | copper/silver export system membrane fusion protein |
| RA | 684,998 | G→A | F86F (TTC→TTT) | gltL ← | glutamate/aspartate ABC transporter ATP binding subunit |
| RA | 699,852 | A→G | L159L (TTG→CTG) | umpH ← | UMP phosphatase |
| RA | 700,681 | T→C | N305S (AAC→AGC) | nagC ← | DNA‑binding transcriptional dual regulator NagC |
| RA | 701,729 | A→G | R341R (CGT→CGC) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 788,636 | A→G | F68L (TTT→CTT) | galM ← | galactose‑1‑epimerase |
| RA | 869,180 | A→G | N554S (AAC→AGC) | 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 | 911,313 | A→G | C280R (TGC→CGC) | hcr ← | NADH oxidoreductase |
| RA | 913,963 | C→T | A299T (GCG→ACG) | lysO ← | L‑lysine exporter |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 950,485 | A→G | L199P (CTT→CCT) | pflA ← | pyruvate formate‑lyase activating enzyme |
| RA | 990,058 | A→G | V100A (GTG→GCG) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,084,789 | G→A | intergenic (+142/‑203) | efeB → / → phoH | heme‑containing peroxidase/deferrochelatase/ATP‑binding protein PhoH |
| RA | 1,086,797 | T→C | V350V (GTA→GTG) | pgaC ← | poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaC |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,147,278 | A→G | N162S (AAC→AGC) | yceD → | DUF177 domain‑containing protein YceD |
| RA | 1,158,446 | T→C | V193A (GTT→GCT) | ptsG → | glucose‑specific PTS enzyme IIBC component |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,225,698 | A→G | I128T (ATA→ACA) | minC ← | Z‑ring positioning protein MinC |
| RA | 1,262,390 | A→C | V163G (GTG→GGG) | ispE ← | 4‑(cytidine 5'‑diphospho)‑2‑C‑methyl‑D‑erythritol kinase |
| RA | 1,263,895 | A→G | E61G (GAG→GGG) | hemA → | glutamyl‑tRNA reductase |
| RA | 1,347,256 | A→G | F553L (TTC→CTC) | rnb ← | RNase II |
| RA | 1,379,930 | T→C | L683L (TTA→CTA) | ycjT → | kojibiose phosphorylase |
| RA | 1,440,705 | (G)5→6 | coding (80/3525 nt) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,473,188 | G→A | pseudogene (2670/3495 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,491,418 | C→T | R173C (CGT→TGT) | cybB → | cytochrome b561 |
| RA | 1,528,423 | A→G | pseudogene (534/2049 nt) | rhsE → | RhsE protein in rhs element |
| RA | 1,530,785 | G→A | pseudogene (200/1054 nt) | yncI → | putative transposase YncI |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,541,821 | A→G | V257A (GTA→GCA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,555,706 | (G)6→7 | intergenic (‑37/+120) | maeA ← / ← sra | malate dehydrogenase, NAD‑requiring/30S ribosomal subunit protein S22 |
| RA | 1,580,584 | (A)6→7 | coding (207/1158 nt) | ydeM ← | putative anaerobic sulfatase maturation enzyme YdeM |
| RA | 1,585,883 | A→G | L202L (TTG→CTG) | ydeP ← | putative oxidoreductase YdeP |
| RA | 1,594,961 | (C)5→6 | pseudogene (3126/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,601,831 | (A)7→8 | coding (342/1536 nt) | lsrA → | Autoinducer‑2 ABC transporter ATP binding subunit |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,677,810 | T→C | T32A (ACC→GCC) | pntA ← | pyridine nucleotide transhydrogenase subunit alpha |
| RA | 1,681,748 | A→G | C95R (TGT→CGT) | ydgC ← | GlpM family protein |
| RA | 1,684,414 | G→A | P52P (CCG→CCA) | tus → | DNA replication terminus site‑binding protein |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,749,951 | T→C | D133G (GAT→GGT) | ydhU ← | putative cytochrome YdhU |
| RA | 1,760,996 | T→C | S266G (AGC→GGC) | sufD ← | Fe‑S cluster scaffold complex subunit SufD |
| RA | 1,793,268 | A→C | H97Q (CAT→CAG) | btuD ← | vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,824,517 | Δ1 bp | coding (421/576 nt) | ves ← | HutD family protein Ves |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,877,795 | G→A | L27L (CTG→CTA) | dgcP → | 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 | 1,908,667 | (A)5→6 | coding (100/144 nt) | mgrB ← | PhoQ kinase inhibitor |
| RA | 1,915,005 | T→C | H177R (CAC→CGC) | proQ ← | RNA chaperone ProQ |
| RA | 1,967,608 | C→T | G298G (GGG→GGA) | cheB ← | protein‑glutamate methylesterase/protein glutamine deamidase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,045,808 | A→G | S291G (AGC→GGC) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,074,362 | (C)6→5 | coding (2824/3120 nt) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,100,008 | A→G | F421L (TTC→CTC) | gnd ← | 6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,103,423 | C→T | E363K (GAA→AAA) | wbbK ← | putative lipopolysaccharide biosynthesis protein |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,237,763 | +C | intergenic (‑10/+6) | mglC ← / ← mglA | D‑galactose/methyl‑galactoside ABC transporter membrane subunit/D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit |
| RA | 2,241,995 | G→C | H325D (CAC→GAC) | yeiB ← | DUF418 domain‑containing protein YeiB |
| RA | 2,248,786 | G→A | A278V (GCG→GTG) | yeiE ← | putative LysR‑type transcriptional regulator YeiE |
| RA | 2,296,418 | T→C | T203A (ACC→GCC) | ccmB ← | heme trafficking system membrane protein CcmB |
| RA | 2,302,575 | T→C | Q60R (CAG→CGG) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,364,598 | T→C | G15G (GGT→GGC) | nudI → | pyrimidine deoxynucleotide diphosphatase NudI |
| RA | 2,397,521 | A→G | V882A (GTG→GCG) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,413,425 | G→A | intergenic (‑293/‑45) | yfbV ← / → ackA | UPF0208 membrane protein YfbV/acetate kinase |
| RA | 2,414,845 | T→C | R33R (CGT→CGC) | pta → | phosphate acetyltransferase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,447,788 | T→C | D218G (GAC→GGC) | prmB ← | 50S ribosomal subunit protein L3 N(5)‑glutamine methyltransferase |
| RA | 2,478,963 | C→T | P373S (CCC→TCC) | dsdX → | D‑serine transporter |
| RA | 2,525,486 | T→C | G120G (GGT→GGC) | yfeN → | conserved outer membrane protein YfeN |
| RA | 2,527,503 | T→C | G186G (GGT→GGC) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,633,928 | G→A | A48V (GCA→GTA) | guaB ← | inosine 5'‑monophosphate dehydrogenase |
| RA | 2,654,466 | A→G | D156D (GAT→GAC) | sseB ← | protein SseB |
| RA | 2,655,114 | T→C | G415G (GGA→GGG) | pepB ← | aminopeptidase B |
| RA | 2,713,559 | (A)7→8 | coding (664/1335 nt) | srmB → | ATP‑dependent RNA helicase SrmB |
| MC JC | 2,720,852 | Δ5 bp | coding (900‑904/2661 nt) | patZ → | peptidyl‑lysine acetyltransferase |
| RA | 2,764,942 | T→C | D71G (GAC→GGC) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| RA | 2,802,048 | T→C | V234A (GTG→GCG) | nrdE → | ribonucleoside‑diphosphate reductase 2 subunit alpha |
| 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 | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,009,222 | T→C | G153G (GGT→GGC) | ygeY → | putative peptidase YgeY |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,083,348 | G→A | A150A (GCC→GCT) | speB ← | agmatinase |
| RA | 3,239,569 | A→G | intergenic (+24/‑375) | alx → / → sstT | putative membrane‑bound redox modulator Alx/serine/threonine:Na(+) symporter |
| RA | 3,263,761 | A→G | R419R (CGT→CGC) | tdcC ← | threonine/serine:H(+) symporter |
| RA | 3,307,295 | G→A | T189I (ACC→ATC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | 3,316,212 | +C | coding (1315/1488 nt) | nusA ← | transcription termination/antitermination protein NusA |
| RA | 3,332,680 | (C)6→7 | coding (56/966 nt) | yhbE ← | inner membrane protein YhbE |
| 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 | 3,418,512 | Δ1 bp | coding (123/222 nt) | yhdV → | lipoprotein YhdV |
| RA | 3,432,994 | (C)6→5 | coding (567/1125 nt) | smf ← | protein Smf |
| RA | 3,529,359 | A→G | K4K (AAA→AAG) | hslR → | heat shock protein Hsp15 |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,601,156 | T→C | T311A (ACG→GCG) | ftsX ← | cell division protein FtsX |
| RA | 3,602,485 | T→C | H88R (CAC→CGC) | ftsE ← | cell division protein FtsE |
| RA | 3,676,004 | A→G | T407A (ACT→GCT) | yhjE → | putative transporter YhjE |
| RA | 3,704,005 | T→C | T253A (ACC→GCC) | dppC ← | dipeptide ABC transporter membrane subunit DppC |
| RA | 3,735,698 | G→A | R240R (CGG→CGA) | xylR → | DNA‑binding transcriptional dual regulator XylR |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,825,131 | A→G | Y206C (TAT→TGT) | trmH → | tRNA (Gm18) 2'‑O‑methyltransferase |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,867,326 | C→T | G33S (GGC→AGC) | ibpA ← | small heat shock protein IbpA |
| RA | 3,872,830 | G→A | P57S (CCA→TCA) | dgoD ← | D‑galactonate dehydratase |
| RA | 3,908,340 | A→G | S9S (AGT→AGC) | pstB ← | phosphate ABC transporter ATP binding subunit |
| RA | 3,923,642 | A→G | G13G (GGT→GGC) | rsmG ← | 16S rRNA m(7)G527 methyltransferase |
| RA | 4,083,781 | T→C | N681S (AAC→AGC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,122,748 | A→G | S198P (TCT→CCT) | ftsN ← | cell division protein FtsN |
| RA | 4,185,799 | T→C | G150G (GGT→GGC) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,295,358 | C→T | A293V (GCC→GTC) | gltP → | glutamate/aspartate : H(+) symporter GltP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,327,848 | (C)5→6 | coding (714/2229 nt) | crfC → | clamp‑binding sister replication fork colocalization protein |
| RA | 4,406,101 | C→T | intergenic (+116/‑89) | purA → / → nsrR | adenylosuccinate synthetase/DNA‑binding transcriptional repressor NsrR |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,455,281 | T→C | D110G (GAC→GGC) | fbp ← | fructose‑1,6‑bisphosphatase 1 |
| RA | 4,502,018 | (A)6→5 | intergenic (+429/+85) | yjgZ → / ← insG | KpLE2 phage‑like element; uncharacterized protein YjgZ/KpLE2 phage‑like element; IS4 putative transposase |
| RA | 4,598,703 | C→T | G247R (GGA→AGA) | opgB ← | phosphoglycerol transferase I |
| RA | 4,602,617 | A→G | V81A (GTG→GCG) | yjjP ← | putative succinate exporter YjjP |
| RA | 4,620,680 | A→G | T360A (ACG→GCG) | deoB → | phosphopentomutase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1432381–1432653 | 1433094–1432658 | 6–714 | 30 [25] | [26] 27 | [stfR]–[pinR] | [stfR],tfaR,[pinR] |
| * | * | ÷ | NC_000913 | 3423776–3424233 | 3424528–3424238 | 6–753 | 27 [26] | [26] 27 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 113 (1.160) | 23 (0.270) | 21/242 | 2.6 | 20.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 76 (0.880) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 87 (0.920) | 55/266 | 0.4 | 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 = | 131 (1.340) | 148 (1.530) | 66/272 | 0.2 | 69.0% | 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) | 122 (1.250) | 78/274 | 0.1 | 98.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4542690 | 49 (0.500) | 29 (0.320) | 25/256 | 2.3 | 34.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 65 (0.710) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||