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 | 1,651 | A→G | I439V (ATC→GTC) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 46,123 | C→T | P106L (CCC→CTC) | yaaU → | putative transporter YaaU |
| RA | 69,037 | A→G | F338L (TTT→CTT) | araB ← | ribulokinase |
| RA | 175,133 | A→G | E9E (GAA→GAG) | clcA → | chloride:H(+) antiporter ClcA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 283,339 | A→G | T47A (ACG→GCG) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 292,991 | A→G | intergenic (‑43/+229) | yagK ← / ← yagL | CP4‑6 prophage; uncharacterized protein YagK/CP4‑6 prophage; resolvase‑like catalytic domain‑containing protein YagL |
| RA | 305,808 | T→C | Q337R (CAG→CGG) | ecpD ← | fimbrial adhesin EcpD |
| RA | 370,620 | A→G | H115R (CAC→CGC) | mhpB → | 3‑carboxyethylcatechol 2,3‑dioxygenase |
| RA | 433,958 | C→T | S168S (AGC→AGT) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| RA | 436,973 | T→C | W129R (TGG→CGG) | pgpA → | phosphatidylglycerophosphatase A |
| RA | 441,118 | T→C | T76A (ACA→GCA) | xseB ← | exodeoxyribonuclease VII subunit XseB |
| RA | 453,781 | G→A | I129I (ATC→ATT) | yajG ← | putative lipoprotein YajG |
| RA | 516,908 | T→C | V109A (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 | 545,941 | A→G | D141D (GAT→GAC) | allD ← | ureidoglycolate dehydrogenase |
| RA | 606,051 | A→G | L50P (CTT→CCT) | ybdJ ← | DUF1158 domain‑containing protein YbdJ |
| RA | 801,601 | T→C | G281G (GGT→GGC) | ybhH → | putative isomerase YbhH |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 932,991 | (G)5→6 | coding (397/495 nt) | lrp → | DNA‑binding transcriptional dual regulator Lrp |
| RA | 950,582 | G→A | R167C (CGC→TGC) | pflA ← | pyruvate formate‑lyase activating enzyme |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,066,280 | A→G | V232V (GTA→GTG) | agp → | glucose‑1‑phosphatase |
| RA | 1,088,526 | T→C | A444A (GCA→GCG) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase |
| RA | 1,112,537 | T→C | W559R (TGG→CGG) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| RA | 1,131,098 | A→G | A27A (GCA→GCG) | flgB → | flagellar basal‑body rod protein FlgB |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,159,061 | C→T | T398I (ACC→ATC) | ptsG → | glucose‑specific PTS enzyme IIBC component |
| RA | 1,166,958 | C→T | R292C (CGT→TGT) | ndh → | NADH:quinone oxidoreductase II |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,227,278 | A→G | S65S (AGT→AGC) | pliG ← | inhibitor of g‑type lysozyme |
| RA | 1,388,183 | A→G | K488K (AAA→AAG) | tyrR → | DNA‑binding transcriptional dual regulator TyrR |
| RA | 1,401,564 | A→G | S70S (AGT→AGC) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
| RA | 1,422,369 | T→C | G129G (GGT→GGC) | ydaV → | Rac prophage; putative ATP‑binding protein YdaV |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,565,109 | G→A | Q209* (CAG→TAG) | dosP ← | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP |
| RA | 1,570,869 | A→G | Y393H (TAT→CAT) | gadB ← | glutamate decarboxylase B |
| RA | 1,597,119 | T→C | pseudogene (968/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,599,375 | G→A | Q279* (CAA→TAA) | lsrK ← | autoinducer‑2 kinase |
| RA | 1,606,759 | A→G | V220V (GTA→GTG) | lsrF → | 3‑hydroxy‑2,4‑pentadione 5‑phosphate thiolase |
| RA | 1,613,520 | G→A | A395V (GCG→GTG) | sad ← | NAD(+)‑dependent succinate semialdehyde dehydrogenase |
| 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 | 1,728,350 | T→C | S2P (TCC→CCC) | rnt → | RNase T |
| RA | 1,835,114 | T→C | W103R (TGG→CGG) | ydjZ → | DedA family protein YdjZ |
| RA | 1,839,309 | T→C | V188A (GTT→GCT) | ynjD → | putative ABC transporter ATP‑binding protein YnjD |
| RA | 1,868,951 | (G)6→5 | intergenic (+109/‑4) | yeaG → / → yeaH | protein kinase YeaG/DUF444 domain‑containing protein YeaH |
| RA | 1,870,127 | T→C | H391H (CAT→CAC) | yeaH → | DUF444 domain‑containing protein YeaH |
| 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 | 1,888,830 | A→G | V306A (GTT→GCT) | fadD ← | fatty acyl‑CoA synthetase |
| RA | 1,972,742 | A→G | intergenic (‑51/+94) | tar ← / ← cheW | methyl‑accepting chemotaxis protein Tar/chemotaxis protein CheW |
| RA | 1,977,215 | (A)8→7 | intergenic (‑76/+51) | motA ← / ← flhC | motility protein A/DNA‑binding transcriptional dual regulator FlhC |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,988,106 | (C)6→7 | intergenic (‑147/‑116) | azuC ← / → yecR | uncharacterized protein AzuC/lipoprotein YecR |
| RA | 2,012,563 | (G)6→7 | pseudogene (62/279 nt) | intG → | putative defective phage integrase |
| RA | 2,047,787 | C→T | T950T (ACC→ACT) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,050,172 | A→G | K1745K (AAA→AAG) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,065,747 | (C)6→7 | coding (18/546 nt) | cobU ← | cobinamide‑P guanylyltransferase/cobinamide kinase |
| RA | 2,104,094 | A→G | I139T (ATA→ACA) | wbbK ← | putative lipopolysaccharide biosynthesis protein |
| RA | 2,135,617 | T→C | V12V (GTA→GTG) | wzc ← | protein‑tyrosine kinase Wzc |
| RA | 2,141,871 | A→G | R115R (CGT→CGC) | dcd ← | dCTP deaminase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,205,386 | T→C | V264A (GTC→GCC) | yehL → | putative AAA(+) MoxR family ATPase YehL |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,544,300 | G→A | F108F (TTC→TTT) | ucpA ← | putative oxidoreductase |
| RA | 2,574,205 | G→A | A34V (GCC→GTC) | eutT ← | putative ethanolamine utilization cobalamin adenosyltransferase |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,633,034 | T→C | D346G (GAC→GGC) | guaB ← | inosine 5'‑monophosphate dehydrogenase |
| RA | 2,634,926 | T→C | V232A (GTT→GCT) | xseA → | exodeoxyribonuclease VII subunit XseA |
| RA | 2,675,181 | G→A | A194V (GCG→GTG) | yphC ← | putative zinc‑binding dehydrogenase YphC |
| RA | 2,703,198 | T→C | T63T (ACA→ACG) | era ← | 30S ribosomal subunit maturation GTPase Era |
| 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 | 2,871,475 | T→C | A102A (GCA→GCG) | ispF ← | 2‑C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,974,973 | T→A | I348F (ATC→TTC) | aas ← | acyltransferase |
| RA | 2,985,665 | (A)7→6 | intergenic (‑73/‑182) | yqeF ← / → yqeG | putative acyltransferase/putative transporter YqeG |
| RA | 3,000,775 | A→G | N144S (AAC→AGC) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,047,411 | C→T | G544D (GGT→GAT) | gcvP ← | glycine decarboxylase |
| RA | 3,063,994 | T→C | M1T (ATG→ACG) † | scpB → | methylmalonyl‑CoA decarboxylase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,101,115 | T→C | D170G (GAC→GGC) | yggN ← | putative EcfF |
| RA | 3,103,886 | C→T | H292Y (CAT→TAT) | mutY → | adenine DNA glycosylase |
| RA | 3,167,586 | T→C | T45A (ACG→GCG) | ygiS ← | putative deoxycholate binding periplasmic protein |
| RA | 3,213,490 | C→T | Y148Y (TAC→TAT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,220,521 | C→T | A343V (GCG→GTG) | patA → | putrescine aminotransferase |
| RA | 3,279,899 | A→G | E329G (GAA→GGA) | kbaZ → | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ |
| RA | 3,293,977 | T→C | V193A (GTG→GCG) | lpoA → | outer membrane lipoprotein ‑ activator of MrcA activity |
| RA | 3,320,229 | T→C | D462G (GAT→GGT) | yhbX ← | putative hydrolase, inner membrane |
| RA | 3,336,740 | A→G | S22P (TCC→CCC) | ibaG ← | acid stress protein IbaG |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,367,249 | T→C | Y108Y (TAT→TAC) | yhcF → | DUF1120 domain‑containing protein YhcF |
| RA | 3,374,109 | T→C | L127L (TTA→TTG) | nanR ← | DNA‑binding transcriptional dual regulator NanR |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,393,847 | T→C | S804S (TCA→TCG) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,502,625 | A→G | M96V (ATG→GTG) | frlC → | fructoselysine 3‑epimerase |
| RA | 3,552,123 | T→C | G117G (GGA→GGG) | malP ← | maltodextrin phosphorylase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,565,289 | G→A | S431S (AGC→AGT) | glgP ← | glycogen phosphorylase |
| RA | 3,667,698 | A→G | intergenic (‑118/+93) | gadA ← / ← ccp | glutamate decarboxylase A/cytochrome c peroxidase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,857,081 | A→G | F442L (TTC→CTC) | yidJ ← | putative sulfatase/phosphatase |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,929,786 | A→G | G436G (GGT→GGC) | ravA ← | regulatory ATPase RavA |
| RA | 3,931,991 | A→G | T226A (ACG→GCG) | kup → | K(+):H(+) symporter Kup |
| RA | 4,060,843 | (G)6→5 | coding (397/711 nt) | yihL → | putative transcriptional regulator YihL |
| RA | 4,074,149 | A→G | V137V (GTA→GTG) | yihV → | 6‑deoxy‑6‑sulfofructose kinase |
| RA | 4,187,063 | A→G | T572A (ACG→GCG) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,252,701 | C→T | P66S (CCG→TCG) | ubiC → | chorismate lyase |
| RA | 4,290,746 | A→G | T91A (ACC→GCC) | nrfD → | putative menaquinol‑cytochrome c reductase subunit NrfD |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,330,519 | (A)6→5 | coding (18/1503 nt) | proP → | osmolyte:H(+) symporter ProP |
| RA | 4,438,087 | T→C | R127R (CGT→CGC) | ytfI → | protein YtfI |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,546,320 | A→G | T409A (ACA→GCA) | fimD → | type I fimbriae usher protein |
| RA | 4,556,769 | (T)9→8 | coding (116/144 nt) | ytiD → | protein YtiD |
| RA | 4,575,536 | A→G | pseudogene (1402/2721 nt) | yjiV → | putative uncharacterized protein YjiV |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,625,160 | G→A | R89H (CGC→CAC) | serB → | phosphoserine phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423768–3424233 | 3424522–3424239 | 7–755 | 12 [10] | [10] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 46 (0.900) | 10 (0.220) | 10/244 | 2.4 | 21.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 34 (0.760) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 45 (0.910) | 33/268 | 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 = | 91 (1.790) | 52 (1.030) | 41/274 | 0.2 | 53.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 53 (1.040) | 35/276 | 0.3 | 96.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 26 (0.510) | 18 (0.380) | 14/258 | 1.9 | 40.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 28 (0.590) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 26 (0.510) | 10 (0.210) | 9/258 | 2.8 | 27.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 28 (0.590) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||