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 | 19,615 | C→T | R301C (CGT→TGT) | nhaR → | DNA‑binding transcriptional activator NhaR |
| RA | 249,970 | G→A | pseudogene (101/1713 nt) | lfhA ← | flagellar system protein, promoterless fragment |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC | 279,931 | Δ11,471 bp | between IS1 | yagB–insA‑3 | yagB, yagA, yagE, yagF, yagG, yagH, xynR, argF, ykgS, insB‑3, insA‑3 |
| RA | 296,077 | A→G | T340T (ACT→ACC) | intF ← | CP4‑6 prophage; putative phage integrase |
| RA | 350,112 | C→T | T34I (ACC→ATC) | prpC → | 2‑methylcitrate synthase |
| RA | 352,853 | C→T | R50* (CGA→TGA) | prpE → | propionyl‑CoA synthetase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 395,690 | C→T | G200S (GGC→AGC) | ampH ← | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| RA | 414,639 | A→G | F372S (TTC→TCC) | sbcC ← | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| RA | 436,703 | A→G | T39A (ACG→GCG) | pgpA → | phosphatidylglycerophosphatase A |
| RA | 507,713 | A→G | V123A (GTT→GCT) | ybaP ← | TraB family protein YbaP |
| RA | 517,337 | T→C | V252A (GTG→GCG) | fetB → | putative iron ABC exporter membrane subunit FetB |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 576,628 | T→C | pseudogene (198/1040 nt) | nmpC ← | DLP12 prophage; putative outer membrane porin NmpC |
| RA | 724,394 | A→G | R7R (CGT→CGC) | kdpD ← | sensory histidine kinase KdpD |
| RA | 800,297 | A→G | G93G (GGT→GGC) | ybhD ← | putative DNA‑binding transcriptional regulator YbhD |
| 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 | 895,717 | A→G | T243A (ACC→GCC) | potG → | putrescine ABC transporter ATP binding subunit |
| RA | 914,242 | A→G | Y206H (TAT→CAT) | lysO ← | L‑lysine exporter |
| RA | 923,255 | (G)5→6 | intergenic (+22/‑9) | clpS → / → clpA | specificity factor for ClpA‑ClpP chaperone‑protease complex/ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| 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 | 1,071,788 | C→T | A124A (GCG→GCA) | rutC ← | putative aminoacrylate peracid reductase |
| RA | 1,084,404 | C→T | S343S (AGC→AGT) | efeB → | heme‑containing peroxidase/deferrochelatase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,207,942 | (G)7→9 | coding (442/630 nt) | ycfK → | e14 prophage; protein StfP |
| RA | 1,208,053 | A→G | T185A (ACA→GCA) | ycfK → | e14 prophage; protein StfP |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,327,340 | A→G | E163E (GAA→GAG) | rluB → | 23S rRNA pseudouridine(2605) synthase |
| RA | 1,342,321 | A→G | E134G (GAA→GGA) | pyrF → | orotidine‑5'‑phosphate decarboxylase |
| RA | 1,351,197 | C→T | intergenic (‑158/+210) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,392,949 | A→G | intergenic (+59/‑278) | pgrR → / → mppA | DNA‑binding transcriptional repressor PgrR/murein tripeptide ABC transporter periplasmic binding protein |
| RA | 1,426,575 | G→T | S41I (AGC→ATC) | ynaA → | Rac prophage; putative prophage tail length tape measure domain‑containing protein YnaA |
| RA | 1,453,961 | C→T | A12V (GCC→GTC) | paaA → | phenylacetyl‑CoA 1,2‑epoxidase, monooxygenase subunit |
| RA | 1,464,003 | A→G | T155T (ACA→ACG) | paaX → | DNA‑binding transcriptional repressor PaaX |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,575,399 | T→C | T741A (ACG→GCG) | yddB ← | putative TonB‑dependent receptor |
| RA | 1,597,313 | (C)7→8 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,598,771 | C→T | R480H (CGC→CAC) | lsrK ← | autoinducer‑2 kinase |
| RA | 1,600,066 | T→C | V48V (GTA→GTG) | lsrK ← | autoinducer‑2 kinase |
| RA | 1,605,121 | T→C | V24A (GTG→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 | 1,659,873 | A→G | Y602C (TAC→TGC) | ynfE → | putative selenate reductase YnfE |
| RA | 1,668,519 | T→C | T16A (ACC→GCC) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,709,258 | (T)6→7 | coding (117/1059 nt) | rsxD → | SoxR [2Fe‑2S] reducing system protein RsxD |
| RA | 1,709,822 | G→A | W227* (TGG→TGA) | rsxD → | SoxR [2Fe‑2S] reducing system protein RsxD |
| RA | 1,710,659 | T→C | G152G (GGT→GGC) | rsxG → | SoxR [2Fe‑2S] reducing system protein RsxG |
| RA | 1,727,494 | (G)6→7 | coding (836/1098 nt) | nemA → | N‑ethylmaleimide reductase |
| RA | 1,730,354 | T→C | V423A (GTA→GCA) | lhr → | putative ATP‑dependent helicase Lhr |
| RA | 1,787,733 | G→A | V97I (GTT→ATT) | ppsR → | posphoenolpyruvate synthetase regulatory protein |
| RA | 1,790,055 | (C)5→6 | coding (1190/1437 nt) | ydiU ← | UPF0061 family protein YdiU |
| RA | 1,800,484 | T→C | D52G (GAC→GGC) | infC ← | translation initiation factor IF‑3 |
| RA | 1,846,611 | T→C | D117G (GAC→GGC) | topB ← | DNA topoisomerase III |
| RA | 1,860,480 | A→G | F285L (TTC→CTC) | ydjL ← | putative zinc‑binding dehydrogenase YdjL |
| RA | 1,870,885 | A→G | Q167Q (CAA→CAG) | cdgI → | putative c‑di‑GMP binding protein CdgI |
| 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 | 1,892,742 | T→C | N165S (AAC→AGC) | yoaA ← | putative 5' to 3' DNA helicase implicated in DNA repair |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,046,454 | T→C | V506A (GTC→GCC) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,058,589 | C→T | A420T (GCT→ACT) | yeeO ← | FMN/FAD exporter |
| RA | 2,094,819 | G→A | L95L (TTG→TTA) | hisH → | imidazole glycerol phosphate synthase subunit HisH |
| RA | 2,166,814 | T→C | F383L (TTC→CTC) | yegQ → | putative peptidase YegQ |
| RA | 2,167,896 | C→T | intergenic (‑76/+93) | yegZ ← / ← yegR | phage protein D/uncharacterized protein YegR |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,279,635 | T→C | V42V (GTA→GTG) | bcr ← | multidrug efflux pump Bcr |
| RA | 2,327,646 | T→C | E166E (GAA→GAG) | yfaP ← | DUF2135 domain‑containing protein YfaP |
| RA | 2,365,433 | T→C | E63G (GAA→GGA) | ais ← | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,832 | T→C | intergenic (+186/‑180) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,502,049 | A→G | F813L (TTT→CTT) | fryA ← | putative PTS multiphosphoryl transfer protein FryA |
| RA | 2,518,016 | (C)5→6 | intergenic (‑184/+25) | pdeA ← / ← alaX | putative c‑di‑GMP phosphodiesterase PdeA/tRNA‑Ala |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,574,588 | T→C | E139G (GAG→GGG) | eutQ ← | putative ethanolamine utilization protein EutQ |
| RA | 2,652,429 | T→C | intergenic (‑142/‑65) | yfhM ← / → sseA | alpha2‑macroglobulin/3‑mercaptopyruvate sulfurtransferase |
| RA | 2,695,809 | (A)6→5 | coding (9/1557 nt) | mltF → | membrane‑bound lytic murein transglycosylase F |
| RA | 2,698,405 | G→A | A49V (GCC→GTC) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,740,847 | T→C | T102A (ACT→GCT) | aroF ← | 3‑deoxy‑7‑phosphoheptulonate synthase, Tyr‑sensitive |
| RA | 2,770,058 | T→C | V119A (GTT→GCT) | yfjR → | CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| 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 | 2,883,264 | T→C | E292G (GAG→GGG) | casA ← | type I‑E CRISPR system Cascade subunit CasA |
| RA | 2,923,326 | T→C | E153E (GAA→GAG) | truC ← | tRNA pseudouridine(65) synthase |
| RA | 2,932,800 | T→C | T72A (ACA→GCA) | fucO ← | L‑1,2‑propanediol oxidoreductase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,960,168 | T→C | Y754C (TAC→TGC) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,968,718 | T→C | D87G (GAC→GGC) | rppH ← | RNA pyrophosphohydrolase |
| RA | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,052,840 | G→A | P227S (CCA→TCA) | ubiH ← | 2‑octaprenyl‑6‑methoxyphenol hydroxylase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,154,181 | A→G | T207A (ACG→GCG) | yghB → | DedA family protein YghB |
| RA | 3,180,089 | C→T | Q116* (CAA→TAA) | ygiB → | DUF1190 domain‑containing protein YgiB |
| RA | 3,205,652 | Δ1 bp | coding (605/933 nt) | ttdR ← | DNA‑binding transcriptional activator Dan |
| RA | 3,213,718 | A→G | L224L (CTA→CTG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,309,913 | T→C | D419G (GAC→GGC) | pnp ← | polynucleotide phosphorylase |
| RA | 3,347,218 | T→C | V35A (GTG→GCG) | rapZ → | RNase adaptor protein |
| 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 | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,409,589 | A→T | I174F (ATC→TTC) | prmA → | methyltransferase for 50S ribosomal subunit protein L11 |
| RA | 3,475,613 | T→C | S36G (AGC→GGC) | tusD ← | sulfurtransferase complex subunit TusD |
| RA | 3,497,179 | G→A | L59L (TTG→TTA) | nirC → | nitrite transporter NirC |
| RA | 3,503,210 | A→G | Y15C (TAC→TGC) | frlD → | fructoselysine 6‑kinase |
| RA | 3,541,606 | T→C | G400G (GGT→GGC) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,565,981 | (T)7→8 | coding (601/2448 nt) | glgP ← | glycogen phosphorylase |
| RA | 3,567,884 | G→A | G50G (GGC→GGT) | glgA ← | glycogen synthase |
| RA | 3,653,562 | A→G | pseudogene (327/478 nt) | yhiS → | putative uncharacterized protein YhiS |
| RA | 3,686,862 | A→G | V771A (GTG→GCG) | bcsC ← | cellulose biosynthesis protein BcsC |
| RA | 3,757,182 | C→T | A216T (GCA→ACA) | yiaY ← | L‑threonine dehydrogenase |
| RA | 3,802,005 | T→C | intergenic (‑6/+34) | waaJ ← / ← waaO | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase/UDP‑D‑glucose:(glucosyl)LPS alpha‑1,3‑glucosyltransferase |
| RA | 3,804,059 | A→G | F27L (TTC→CTC) | waaB ← | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase |
| 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 | 3,915,448 | (G)6→7 | intergenic (‑248/+105) | glmU ← / ← atpC | fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase/ATP synthase F1 complex subunit epsilon |
| RA | 3,961,849 | C→T | R391R (CGC→CGT) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 4,113,940 | G→A | A178V (GCG→GTG) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,130,798 | T→C | F322L (TTT→CTT) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,300,677 | A→G | R118R (CGT→CGC) | mdtP ← | putative multidrug efflux pump outer membrane channel |
| RA | 4,385,031 | A→G | N398S (AAC→AGC) | yjeM → | putative transporter YjeM |
| RA | 4,386,978 | C→T | W798* (TGG→TAG) | mscM ← | miniconductance mechanosensitive channel MscM |
| RA | 4,395,056 | G→A | G331S (GGC→AGC) | nnr → | NAD(P)HX epimerase/NAD(P)HX dehydratase |
| RA | 4,400,218 | A→G | intergenic (+16/‑70) | miaA → / → hfq | tRNA dimethylallyltransferase/RNA‑binding protein Hfq |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,453,419 | A→G | L283L (CTA→CTG) | ytfT → | galactofuranose ABC transporter putative membrane subunit YtfT |
| RA | 4,495,421 | C→T | A263A (GCG→GCA) | ahr ← | aldehyde reductase, NADPH‑dependent |
| RA | 4,504,834 | A→G | I259M (ATA→ATG) | yjhB → | putative sialic acid transporter |
| RA | 4,509,374 | A→G | pseudogene (366/471 nt) | insO → | KpLE2 phage‑like element; IS911B regulator fragment |
| RA | 4,547,614 | C→T | A840V (GCG→GTG) | fimD → | type I fimbriae usher protein |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,606,330 | (G)8→7 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 226408–226603 | 228561–226989 | 387–2154 | 12 [11] | [8] 12 | rrlH | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 3423785–3424233 | 3424525–3424238 | 6–741 | 12 [10] | [8] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3762388–3764072 | 3765187–3764077 | 6–2800 | 13 [10] | [11] 12 | rhsA | rhs element protein RhsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 50 (0.940) | 36/266 | 0.3 | 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 = | 70 (1.280) | 71 (1.300) | 45/272 | 0.1 | 66.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.060) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 54 (0.990) | 41/274 | 0.2 | 93.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.070) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||