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 | 7,332 | A→G | L210L (TTG→CTG) | yaaJ ← | putative transporter YaaJ |
| RA | 40,150 | A→G | R79R (CGT→CGC) | caiA ← | crotonobetainyl‑CoA reductase |
| RA | 43,832 | A→G | E215E (GAA→GAG) | fixB → | putative electron transfer flavoprotein FixB |
| RA | 125,335 | A→G | E773E (GAA→GAG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 179,815 | G→A | V193V (GTG→GTA) | dgt → | dGTP triphosphohydrolase |
| RA | 215,896 | A→G | T210A (ACC→GCC) | nlpE → | lipoprotein NlpE |
| 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 | 342,414 | C→T | D430D (GAC→GAT) | yahJ → | putative deaminase with metallo‑dependent hydrolase domain |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 425,874 | C→T | F288F (TTC→TTT) | queA → | tRNA preQ1(34) S‑adenosylmethionine ribosyltransferase‑isomerase |
| RA | 452,412 | T→C | A378A (GCA→GCG) | ampG ← | muropeptide:H(+) symporter |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 550,392 | A→G | T256A (ACG→GCG) | ylbF → | DUF2877 domain‑containing protein YlbF |
| RA | 633,496 | T→C | intergenic (‑19/‑90) | hcxA ← / → ybdL | hydroxycarboxylate dehydrogenase A/methionine‑oxo‑acid transaminase, PLP‑dependent |
| RA | 676,304 | T→C | N82D (AAT→GAT) | ybeQ ← | Sel1 repeat‑containing protein YbeQ |
| RA | 711,377 | A→G | V30A (GTT→GCT) | fldA ← | flavodoxin 1 |
| RA | 749,154 | A→G | V185A (GTT→GCT) | ybgP ← | putative fimbrial chaperone YbgP |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 911,203 | (C)5→6 | coding (948/969 nt) | hcr ← | NADH oxidoreductase |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 985,846 | (A)8→7 | intergenic (‑137/+48) | aspC ← / ← ompF | aspartate aminotransferase/outer membrane porin F |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,018,976 | (A)8→9 | intergenic (+39/+37) | matP → / ← ompA | macrodomain Ter protein/outer membrane porin A |
| RA | 1,028,007 | C→T | A21V (GCA→GTA) | yccU → | putative CoA‑binding protein with NAD(P)‑binding Rossmann‑fold domain |
| RA | 1,114,747 | T→C | E248E (GAA→GAG) | mdtG ← | efflux pump MdtG |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,184,099 | T→C | T116A (ACC→GCC) | potB ← | spermidine preferential ABC transporter membrane subunit PotB |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,262,821 | A→G | G19G (GGT→GGC) | ispE ← | 4‑(cytidine 5'‑diphospho)‑2‑C‑methyl‑D‑erythritol kinase |
| RA | 1,263,632 | (G)5→6 | intergenic (‑132/‑82) | lolB ← / → hemA | outer membrane lipoprotein LolB/glutamyl‑tRNA reductase |
| RA | 1,273,790 | C→T | R3C (CGT→TGT) | ychO → | putative invasin YchO |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,352,307 | T→C | I110V (ATT→GTT) | sapF ← | putrescine ABC exporter ATP binding protein SapF |
| RA | 1,422,015 | A→G | E11E (GAA→GAG) | ydaV → | Rac prophage; putative ATP‑binding protein YdaV |
| RA | 1,431,974 | A→G | T976A (ACC→GCC) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,435,192 | A→G | V143A (GTG→GCG) | uspF ← | nucleotide binding filament protein |
| RA | 1,460,302 | A→G | T417A (ACC→GCC) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase |
| RA | 1,471,279 | A→G | pseudogene (761/3495 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,576,345 | A→T | Y425* (TAT→TAA) | yddB ← | putative TonB‑dependent receptor |
| RA | 1,580,434 | (G)5→4 | coding (357/1158 nt) | ydeM ← | putative anaerobic sulfatase maturation enzyme YdeM |
| RA | 1,597,313 | (C)7→8 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,606,990 | A→G | intergenic (+15/‑9) | lsrF → / → lsrG | 3‑hydroxy‑2,4‑pentadione 5‑phosphate thiolase/(4S)‑4‑hydroxy‑5‑phosphonooxypentane‑2,3‑dione isomerase |
| RA | 1,617,357 | T→C | G110G (GGT→GGC) | ydeA → | L‑arabinose exporter |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,647,973 | T→C | Y14H (TAT→CAT) | dicA → | DNA‑binding transcriptional dual regulator DicA |
| RA | 1,681,793 | T→C | T80A (ACC→GCC) | ydgC ← | GlpM family protein |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,767,413 | T→C | T425A (ACC→GCC) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,770,354 | T→C | intergenic (+168/‑18) | ydiK → / → rprA | putative transporter YdiK/small regulatory RNA RprA |
| RA | 1,781,798 | T→C | V135A (GTT→GCT) | ydiS → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
| RA | 1,781,906 | G→A | G171E (GGA→GAA) | ydiS → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
| RA | 1,793,058 | C→T | A167A (GCG→GCA) | btuD ← | vitamin B12 ABC transporter ATP binding subunit |
| 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 | 1,959,539 | (T)5→4 | coding (308/567 nt) | yecM ← | putative metal‑binding enzyme YecM |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,987,851 | (A)7→6 | intergenic (‑93/+22) | yecJ ← / ← azuC | DUF2766 domain‑containing protein YecJ/uncharacterized protein AzuC |
| RA | 2,018,925 | (C)5→6 | coding (540/1128 nt) | fliK → | flagellar hook‑length control protein |
| RA | 2,035,380 | A→G | intergenic (+137/‑455) | yedS → / → hchA | putative outer membrane protein YedS, N‑terminal fragment/protein/nucleic acid deglycase 1 |
| RA | 2,132,087 | G→A | R157* (CGA→TGA) | wcaB ← | putative colanic acid biosynthesis acyl transferase |
| RA | 2,139,032 | G→A | V377V (GTG→GTA) | yegH → | inner membrane protein YegH |
| RA | 2,159,983 | T→C | L533P (CTG→CCG) | 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 | 2,210,343 | T→C | L415P (CTG→CCG) | yehQ → | SWIM zinc finger domains‑containing protein YehQ |
| RA | 2,239,585 | A→G | V255A (GTG→GCG) | mglB ← | D‑galactose/methyl‑galactoside ABC transporter periplasmic binding protein |
| RA | 2,293,774 | C→A | K377N (AAG→AAT) | ccmF ← | holocytochrome c synthetase membrane subunit CcmF |
| RA | 2,329,538 | G→A | P87L (CCG→CTG) | yfaQ ← | tandem DUF2300 domain‑containing protein YfaQ |
| RA | 2,362,020 | A→G | C64C (TGT→TGC) | yfaX ← | putative DNA‑binding transcriptional regulator YfaX |
| RA | 2,367,459 | A→G | N130S (AAC→AGC) | arnC → | undecaprenyl‑phosphate 4‑deoxy‑4‑formamido‑L‑arabinose transferase |
| RA | 2,429,698 | C→G | A181P (GCT→CCT) | purF ← | amidophosphoribosyltransferase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,583,424 | T→C | T19A (ACC→GCC) | nudK ← | GDP‑mannose hydrolase |
| RA | 2,634,926 | T→C | V232A (GTT→GCT) | xseA → | exodeoxyribonuclease VII subunit XseA |
| RA | 2,646,693 | C→T | W211* (TGG→TGA) | pbpC ← | peptidoglycan glycosyltransferase PbpC |
| RA | 2,733,433 | A→G | A247A (GCT→GCC) | clpB ← | ClpB chaperone |
| RA | 2,776,424 | T→C | L13L (CTT→CTC) | yfjY → | CP4‑57 prophage; RadC‑like JAB domain‑containing protein YfjY |
| RA | 2,776,903 | A→G | A9A (GCA→GCG) | ypjJ → | CP4‑57 prophage; DUF987 domain‑containing protein YpjJ |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,830,382 | A→G | A190A (GCA→GCG) | gutQ → | D‑arabinose 5‑phosphate isomerase GutQ |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,927,670 | T→C | *455Q (TAA→CAA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,953,118 | C→T | L962L (CTG→CTA) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,972,909 | (C)6→7 | coding (954/1194 nt) | lplT ← | lysophospholipid transporter |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,219,401 | T→C | intergenic (‑325/‑93) | aer ← / → patA | aerotaxis sensor receptor, flavoprotein/putrescine aminotransferase |
| RA | 3,222,686 | T→C | R18R (CGT→CGC) | ebgA → | evolved beta‑D‑galactosidase subunit alpha |
| RA | 3,240,120 | (C)5→4 | coding (177/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,249,538 | G→A | G55D (GGT→GAT) | yqjD → | ribosome‑ and membrane‑associated DUF883 domain‑containing protein YqjD |
| RA | 3,270,306 | T→C | noncoding (287/377 nt) | rnpB ← | RNase P catalytic RNA component |
| RA | 3,270,321 | A→G | noncoding (272/377 nt) | rnpB ← | RNase P catalytic RNA component |
| RA | 3,300,468 | G→A | L97L (CTC→CTT) | yhbS ← | putative acyltransferase with acyl‑CoA N‑acyltransferase domain |
| RA | 3,342,107 | (G)6→7 | coding (842/987 nt) | kdsD → | D‑arabinose 5‑phosphate isomerase KdsD |
| RA | 3,348,682 | T→C | G77G (GGT→GGC) | yrbL → | protein kinase‑like domain‑containing protein YrbL |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,375,008 | T→C | V47A (GTA→GCA) | dcuD → | putative transporter DcuD |
| RA | 3,385,834 | (C)5→6 | intergenic (+33/+23) | yhcN → / ← yhcO | DUF1471 domain‑containing stress‑induced protein YhcN/putative barnase inhibitor |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,430,060 | T→C | E260G (GAA→GGA) | aroE ← | shikimate dehydrogenase |
| RA | 3,551,302 | (T)5→6 | coding (1172/2394 nt) | malP ← | maltodextrin phosphorylase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,814,302 | T→C | V124A (GTA→GCA) | dut → | deoxyuridine triphosphatase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,850,287 | (T)5→4 | coding (440/591 nt) | uhpA ← | DNA‑binding transcriptional activator UhpA |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,867,068 | T→C | I119V (ATC→GTC) | ibpA ← | small heat shock protein IbpA |
| RA | 3,870,649 | A→G | V361A (GTT→GCT) | dgoT ← | putative D‑galactonate transporter |
| RA | 3,997,603 | C→T | P141S (CCG→TCG) | yigB → | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase |
| RA | 4,103,550 | C→T | intergenic (+54/+52) | yiiM → / ← cpxA | 2‑amino‑6‑N‑hydroxylaminopurine resistance protein/sensory histidine kinase CpxA |
| RA | 4,236,119 | A→G | T72A (ACC→GCC) | yjbE → | uncharacterized protein YjbE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,312,203 | (A)7→8 | coding (789/891 nt) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,394,870 | (G)5→6 | coding (805/1548 nt) | nnr → | NAD(P)HX epimerase/NAD(P)HX dehydratase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,474,410 | T→C | V96A (GTA→GCA) | bdcR → | putative transcriptional regulator BdcR |
| RA | 4,529,195 | A→G | V350A (GTC→GCC) | sgcC ← | putative PTS enzyme IIC component SgcC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1529980 | 1530439 | 460 | 31 [30] | [30] 31 | [ydcD]–[yncO] | [ydcD],[yncO] |
| * | * | ÷ | NC_000913 | 2249606 | 2249711 | 106 | 32 [30] | [28] 33 | [yeiE] | [yeiE] |
| * | * | ÷ | NC_000913 | 3413528 | 3413690 | 163 | 31 [30] | [30] 31 | envR/acrE | DNA‑binding transcriptional repressor EnvR/multidrug efflux pump membrane fusion lipoprotein AcrE |
| * | * | ÷ | NC_000913 | 3423738–3424234 | 3424537–3424239 | 6–800 | 31 [30] | [30] 31 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3455400 | 3455604 | 205 | 31 [30] | [30] 31 | [gspC] | [gspC] |
| * | * | ÷ | NC_000913 | 3751881 | 3752056 | 176 | 32 [30] | [30] 35 | [yiaU] | [yiaU] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 67 (0.700) | 66 (0.790) | 40/246 | 0.7 | 56.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 43 (0.510) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 66 (0.690) | 30 (0.360) | 24/246 | 2.1 | 37.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 43 (0.510) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 150 (1.580) | 118 (1.250) | 59/276 | 0.2 | 61.0% | 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) | 93 (0.980) | 49/278 | 0.5 | 93.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 7 (0.070) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||