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 | freq | annotation | gene | description |
| RA | 40,191 | C→G | 6.4% | G66R (GGG→CGG) | caiA ← | crotonobetaine reductase subunit II, FAD‑binding |
| RA | 169,748 | T→A | 5.3% | intergenic (+21/‑30) | fhuA → / → fhuC | ferrichrome outer membrane transporter/iron(3+)‑hydroxamate import ABC transporter ATPase |
| RA | 172,496 | A→G | 5.1% | Q345Q (CAA→CAG) | fhuB → | iron(3+)‑hydroxamate import ABC transporter permease |
| RA | 176,046 | G→T | 5.3% | G314C (GGC→TGC) | clcA → | H(+)/Cl(‑) exchange transporter |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 342,876 | T→C | 6.1% | intergenic (+369/‑8) | yahJ → / → yahK | putative metallo‑dependent hydrolase domain deaminase/broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing |
| RA | 520,603 | T→C | 5.8% | V63A (GTG→GCG) | ybbP → | putative ABC transporter permease |
| RA | 521,669 | C→T | 7.3% | C418C (TGC→TGT) | ybbP → | putative ABC transporter permease |
| RA | 557,009 | C→T | 6.7% | V245M (GTG→ATG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| RA | 561,943 | G→A | 5.3% | T749T (ACG→ACA) | sfmD → | putative outer membrane export usher protein |
| RA | 601,304 | T→C | 7.8% | L864P (CTA→CCA) | cusA → | copper/silver efflux system, membrane component |
| RA | 655,361 | A→G | 5.2% | I203T (ATC→ACC) | dcuC ← | anaerobic C4‑dicarboxylate transport |
| RA | 704,456 | G→A | 6.2% | A171A (GCG→GCA) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 745,001 | T→C | 5.6% | G253G (GGT→GGC) | ybgK → | putative allophanate hydrolase, subunit 2 |
| RA | 815,853 | C→T | 5.7% | A265A (GCG→GCA) | ybhK ← | putative CofD superfamily transferase |
| RA | 854,885 | T→C | 5.7% | D287G (GAC→GGC) | ldtB ← | L,D‑transpeptidase linking Lpp to murein |
| RA | 864,035 | G→A | 5.5% | V132I (GTT→ATT) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 875,393 | C→A | 7.8% | S20* (TCA→TAA) | yliF → | putative membrane‑anchored diguanylate cyclase |
| RA | 908,491 | C→T | 5.8% | A268A (GCG→GCA) | ltaE ← | L‑allo‑threonine aldolase, PLP‑dependent |
| RA | 912,095 | T→A | 5.5% | Q19L (CAA→CTA) | hcr ← | HCP oxidoreductase, NADH‑dependent |
| RA | 929,415 | A→G | 5.3% | L516L (CTT→CTC) | cydD ← | glutathione/cysteine ABC transporter export permease/ATPase |
| RA | 937,718 | G→A | 5.8% | R116H (CGC→CAC) | lolA → | lipoprotein chaperone |
| RA | 946,381 | G→A | 6.5% | G171R (GGG→AGG) | ycaD → | putative MFS transporter, inner membrane protein |
| RA | 954,156 | C→T | 6.6% | R104H (CGC→CAC) | focA ← | formate channel |
| RA | 957,906 | T→C | 5.3% | L85P (CTG→CCG) | serC → | 3‑phosphoserine/phosphohydroxythreonine aminotransferase |
| RA | 974,964 | C→T | 7.7% | R216C (CGT→TGT) | mukF → | chromosome condensin MukBEF, kleisin‑like subunit, binds calcium |
| RA | 1,162,830 | G→A | 6.8% | E65K (GAA→AAA) | lpoB → | OM lipoprotein stimulator of MrcB transpeptidase |
| RA | 1,174,843 | A→G | 5.9% | L108P (CTG→CCG) | ycfT ← | inner membrane protein |
| RA | 1,353,880 | G→A | 5.7% | T213T (ACC→ACT) | sapC ← | antimicrobial peptide transport ABC transporter permease |
| RA | 1,397,825 | C→A | 5.9% | V266V (GTG→GTT) | uspE ← | stress‑induced protein |
| RA | 1,435,428 | C→A | 5.7% | L64L (CTG→CTT) | uspF ← | stress‑induced protein, ATP‑binding protein |
| RA | 1,497,981 | G→A | 5.9% | G376S (GGC→AGC) | opgD → | OPG biosynthetic periplasmic protein |
| RA | 1,521,690 | T→C | 5.4% | D459G (GAT→GGT) | yncD ← | putative iron outer membrane transporter |
| RA | 1,555,781 | G→C | 7.1% | intergenic (‑112/+45) | maeA ← / ← sra | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme/stationary‑phase‑induced ribosome‑associated protein |
| RA | 1,555,782 | C→T | 7.1% | intergenic (‑113/+44) | maeA ← / ← sra | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme/stationary‑phase‑induced ribosome‑associated protein |
| RA | 1,555,783 | A→G | 6.9% | intergenic (‑114/+43) | maeA ← / ← sra | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme/stationary‑phase‑induced ribosome‑associated protein |
| RA | 1,555,784 | G→C | 6.6% | intergenic (‑115/+42) | maeA ← / ← sra | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme/stationary‑phase‑induced ribosome‑associated protein |
| RA | 1,631,492 | G→T | 8.6% | pseudogene (794/1284 nt) | ydfJ ← | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein |
| RA | 1,662,350 | C→T | 100% | P599S (CCC→TCC) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,700,680 | C→T | 5.5% | A442A (GCC→GCT) | malX → | maltose and glucose‑specific PTS enzyme IIB component and IIC component |
| RA | 1,708,854 | C→G | 25.8% | Q646E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,738,550 | A→G | 7.7% | Q236R (CAG→CGG) | purR → | transcriptional repressor, hypoxanthine‑binding |
| RA | 1,757,908 | C→T | 5.5% | G273D (GGC→GAC) | ldtE ← | murein L,D‑transpeptidase |
| RA | 1,771,897 | C→A | 5.1% | T276K (ACA→AAA) | ydiM → | putative MFS transporter, membrane protein |
| RA | 1,797,388 | G→T | 5.6% | P186Q (CCG→CAG) | pheT ← | phenylalanine tRNA synthetase, beta subunit |
| RA | 1,806,319 | C→G | 100% | intergenic (‑236/‑51) | ydiY ← / → pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II |
| RA | 1,806,971 | A→C | 18.9% | Q201P (CAG→CCG) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,807,043 | T→A | 65.8% | L225Q (CTG→CAG) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,807,100 | C→T | 6.6% | P244L (CCA→CTA) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,811,349 | A→G | 5.2% | Q139R (CAG→CGG) | ydjN → | putative transporter |
| RA | 1,854,741 | G→A | 5.1% | R38R (CGC→CGT) | ydjF ← | putative DNA‑binding transcriptional regulator |
| RA | 1,894,735 | T→A | 5.9% | intergenic (‑4/‑70) | yoaH ← / → pabB | UPF0181 family protein/aminodeoxychorismate synthase, subunit I |
| RA | 1,898,122 | C→T | 5.0% | A397A (GCC→GCT) | sdaA → | L‑serine dehydratase 1 |
| RA | 1,898,316 | T→C | 6.8% | intergenic (+20/‑111) | sdaA → / → yoaD | L‑serine dehydratase 1/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,898,318 | C→T | 6.9% | intergenic (+22/‑109) | sdaA → / → yoaD | L‑serine dehydratase 1/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,898,319 | A→T | 6.9% | intergenic (+23/‑108) | sdaA → / → yoaD | L‑serine dehydratase 1/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,898,320 | A→G | 6.8% | intergenic (+24/‑107) | sdaA → / → yoaD | L‑serine dehydratase 1/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,898,322 | G→A | 6.7% | intergenic (+26/‑105) | sdaA → / → yoaD | L‑serine dehydratase 1/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,920,827 | T→C | 5.0% | V202A (GTG→GCG) | rsmF → | 16S rRNA m(5)C1407 methyltransferase, SAM‑dependent |
| RA | 1,951,101 | A→G | 5.7% | L90L (TTA→TTG) | yecD → | isochorismatase family protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,988,048 | A→T | 8.2% | intergenic (‑89/‑174) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 1,988,049 | C→T | 8.4% | intergenic (‑90/‑173) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 1,988,050 | A→G | 8.5% | intergenic (‑91/‑172) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 1,988,051 | A→T | 8.5% | intergenic (‑92/‑171) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 2,025,638 | T→A | 5.3% | V43D (GTC→GAC) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,079,261 | T→C | 5.5% | K34R (AAG→AGG) | yeeX ← | UPF0265 family protein |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,188,411 | C→T | 5.8% | E2K (GAA→AAA) | yehA ← | putative fimbrial‑like adhesin protein |
| RA | 2,202,047 | T→C | 6.4% | M590T (ATG→ACG) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,291,283 | T→G | 5.2% | intergenic (+136/+75) | narP → / ← ccmH | response regulator in two‑component regulatory system with NarQ/heme lyase, CcmH subunit |
| RA | 2,291,284 | C→A | 5.0% | intergenic (+137/+74) | narP → / ← ccmH | response regulator in two‑component regulatory system with NarQ/heme lyase, CcmH subunit |
| RA | 2,355,891 | T→C | 7.1% | L124P (CTG→CCG) | glpC → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster |
| RA | 2,357,836 | G→A | 8.0% | pseudogene (33/198 nt) | ypaA → | pseudogene, C‑terminal fragment, Transposase_31 family |
| RA | 2,418,487 | T→C | 5.6% | G469G (GGT→GGC) | yfcC → | putative inner membrane transporter; C4‑dicarboxylate anaerobic carrier family protein |
| RA | 2,419,742 | G→A | 5.8% | A16V (GCG→GTG) | yfcE ← | phosphodiesterase activity on bis‑pNPP |
| RA | 2,422,131 | G→A | 5.6% | A142T (GCT→ACT) | yfcH → | putative NAD‑dependent nucleotide‑sugar epimerase |
| RA | 2,464,601 | G→A | 5.8% | T136M (ACG→ATG) | mlaA ← | ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,502,271 | C→T | 5.7% | V739I (GTT→ATT) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,509,337 | A→G | 6.7% | A30A (GCT→GCC) | glk ← | glucokinase |
| RA | 2,635,061 | C→T | 5.8% | T277I (ACC→ATC) | xseA → | exonuclease VII, large subunit |
| RA | 2,757,419 | T→G | 5.0% | intergenic (+19/+225) | intA → / ← yfjH | CP4‑57 prophage; integrase/CP4‑57 prophage; uncharacterized protein |
| RA | 2,757,421 | T→G | 5.0% | intergenic (+21/+223) | intA → / ← yfjH | CP4‑57 prophage; integrase/CP4‑57 prophage; uncharacterized protein |
| RA | 2,842,195 | A→G | 5.3% | A402A (GCA→GCG) | ascB → | cryptic 6‑phospho‑beta‑glucosidase |
| RA | 3,118,601 | G→A | 8.0% | A171V (GCG→GTG) | sslE ← | putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,148,957 | C→T | 5.1% | intergenic (+20/+20) | gpr → / ← yqhA | L‑glyceraldehyde 3‑phosphate reductase/UPF0114 family putative inner membrane protein |
| RA | 3,270,030 | T→C | 17.0% | intergenic (+428/+186) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,281,021 | G→A | 7.4% | pseudogene (321/375 nt) | agaW → | pseudogene, N‑acetylgalactosamine‑specific enzyme IIC component of PTS;enzyme; Central intermediary metabolism: Amino sugars; PTS system N‑acetylgalactosameine‑specific IIC component 2 |
| RA | 3,331,019 | C→T | 5.3% | D246N (GAT→AAT) | obgE ← | GTPase involved in cell partioning and DNA repair |
| RA | 3,416,545 | C→T | 6.8% | H505Y (CAC→TAC) | acrF → | multidrug efflux system protein |
| RA | 3,451,416 | C→A | 5.4% | G90V (GGC→GTC) | rplW ← | 50S ribosomal subunit protein L23 |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,577,416 | G→A | 6.9% | D59D (GAC→GAT) | gntK ← | gluconate kinase 2 |
| RA | 3,708,427 | G→A | 7.0% | intergenic (‑722/+189) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,428 | T→A | 8.4% | intergenic (‑723/+188) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,429 | T→C | 7.2% | intergenic (‑724/+187) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,743,306 | C→T | 5.4% | Q192* (CAG→TAG) | yiaK → | 2,3‑diketo‑L‑gulonate reductase, NADH‑dependent |
| JC | 3,815,859 | Δ82 bp | 66.4% | [rph]–[rph] | [rph], [rph] | |
| JC | 3,816,605 | Δ103 bp | 13.3% | [yicC] | [yicC] | |
| RA | 3,959,481 | C→G | 5.7% | intergenic (+36/+51) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,023,245 | A→G | 6.2% | E170E (GAA→GAG) | tatC → | TatABCE protein translocation system subunit |
| RA | 4,080,479 | A→G | 5.2% | I250I (ATT→ATC) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,082,066 | C→T | 5.5% | D232N (GAC→AAC) | fdoH ← | formate dehydrogenase‑O, Fe‑S subunit |
| RA | 4,091,644 | G→T | 6.1% | G241G (GGC→GGA) | frvB ← | putative PTS enzyme, IIB component/IIC component |
| RA | 4,133,952 | C→T | 6.1% | Q40* (CAA→TAA) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,134,511 | A→T | 5.4% | Y226F (TAC→TTC) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,188,572 | C→T | 11.9% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,272,763 | C→T | 5.3% | R370H (CGT→CAT) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 4,274,365 | G→T | 5.6% | E81* (GAA→TAA) | ssb → | single‑stranded DNA‑binding protein |
| RA | 4,296,060 | C→T | 42.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,547,305 | T→C | 5.6% | V737A (GTG→GCG) | fimD → | fimbrial usher outer membrane porin protein; FimCD chaperone‑usher |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423750–3424234 | 3424622–3424238 | 5–873 | 33 [32] | [32] 33 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4107521 | 4108521 | 1001 | 35 [31] | [28] 33 | pfkA | pfkA |
| * | * | ÷ | NC_000913 | 4144014 | 4147099 | 3086 | 33 [31] | [29] 33 | [pflD]–[pflC] | [pflD],[pflC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 212286 = | 83 (1.070) | 4 (0.050) | 4/252 | NT | 5.1% | intergenic (+20/‑45) | yaeR/tilS | putative lyase/tRNA(Ile)‑lysidine synthetase |
| ? | NC_000913 | 212307 = | 70 (0.950) | intergenic (+41/‑24) | yaeR/tilS | putative lyase/tRNA(Ile)‑lysidine synthetase | |||||
| * | ? | NC_000913 | 225078 = | NA (NA) | 8 (0.110) | 6/252 | NT | NA | noncoding (1308/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 225100 = | NA (NA) | noncoding (1330/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 540528 | 66 (0.850) | 5 (0.070) | 4/250 | NT | 7.2% | intergenic (+20/‑37) | allB/ybbY | allantoinase/putative uracil/xanthine transporter |
| ? | NC_000913 | = 540537 | 67 (0.920) | intergenic (+29/‑28) | allB/ybbY | allantoinase/putative uracil/xanthine transporter | |||||
| * | ? | NC_000913 | 1207790 = | 22 (0.280) | 25 (0.370) | 24/234 | NT | 50.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 30 (0.440) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 20 (0.260) | 45 (0.660) | 37/234 | NT | 65.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 30 (0.440) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 114 (1.510) | 77/258 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||