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 | 66,733 | A→G | 5.7% | intergenic (‑183/+102) | araD ← / ← araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| RA | 209,609 | T→G | 5.1% | intergenic (+29/‑70) | accA → / → ldcC | acetyl‑CoA carboxylase, carboxytransferase, alpha subunit/lysine decarboxylase 2, constitutive |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 359,089 | T→C | 5.4% | G97G (GGT→GGC) | cynT → | carbonic anhydrase |
| RA | 388,676 | T→G | 5.3% | intergenic (+30/+77) | tauD → / ← hemB | taurine dioxygenase, 2‑oxoglutarate‑dependent/5‑aminolevulinate dehydratase (porphobilinogen synthase) |
| RA | 388,681 | A→C | 5.8% | intergenic (+35/+72) | tauD → / ← hemB | taurine dioxygenase, 2‑oxoglutarate‑dependent/5‑aminolevulinate dehydratase (porphobilinogen synthase) |
| RA | 420,361 | C→T | 5.6% | V257V (GTC→GTT) | brnQ → | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| RA | 695,326 | C→T | 6.0% | R76C (CGT→TGT) | ubiF → | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase |
| RA | 753,309 | G→T | 5.4% | A387E (GCA→GAA) | gltA ← | citrate synthase |
| RA | 814,955 | A→T | 6.2% | H477L (CAC→CTC) | uvrB → | exision nuclease of nucleotide excision repair, DNA damage recognition component |
| RA | 908,975 | G→T | 6.9% | A107D (GCC→GAC) | ltaE ← | L‑allo‑threonine aldolase, PLP‑dependent |
| RA | 1,047,508 | G→A | 5.9% | A146A (GCC→GCT) | gfcD ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,128,199 | G→A | 5.5% | A121T (GCT→ACT) | murJ → | putative lipid II flippase |
| RA | 1,136,706 | G→A | 5.4% | G145S (GGC→AGC) | flgI → | putative flagellar basal body protein |
| RA | 1,148,750 | T→C | 5.7% | intergenic (+59/‑9) | plsX → / → fabH | putative phosphate acyltransferase/3‑oxoacyl‑[acyl‑carrier‑protein] synthase III |
| RA | 1,151,873 | T→A | 5.6% | intergenic (+22/‑66) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,151,874 | T→A | 6.1% | intergenic (+23/‑65) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,178,453 | Δ1 bp | 5.6% | coding (1134/1245 nt) | lolE → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,261,481 | G→C | 100% | A132G (GCT→GGT) | prs ← | phosphoribosylpyrophosphate synthase |
| RA | 1,263,541 | T→C | 5.5% | intergenic (‑41/‑173) | lolB ← / → hemA | lipoprotein localization factor/glutamyl tRNA reductase |
| RA | 1,280,813 | A→G | 6.1% | E317G (GAA→GGA) | narG → | nitrate reductase 1, alpha subunit |
| RA | 1,286,965 | A→G | 9.5% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| JC JC | 1,293,033 | IS1 (+) +9 bp | 100% | intergenic (‑111/‑486) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,315,516 | Δ1 bp | 6.0% | coding (255/501 nt) | yciF ← | putative rubrerythrin/ferritin‑like metal‑binding protein |
| RA | 1,321,962 | T→C | 5.1% | T329A (ACA→GCA) | trpE ← | component I of anthranilate synthase |
| RA | 1,439,191 | C→T | 6.6% | V532M (GTG→ATG) | pfo ← | pyruvate‑flavodoxin oxidoreductase |
| RA | 1,481,585 | T→A | 6.9% | M226K (ATG→AAG) | ynbD → | putative phosphatase inner membrane protein |
| RA | 1,504,968 | Δ1 bp | 5.7% | coding (1113/1176 nt) | ydcO ← | BenE family inner membrane putative transporter |
| RA | 1,552,270 | T→G | 5.3% | intergenic (+279/+128) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,604,638 | C→T | 5.2% | R198C (CGC→TGC) | lsrD → | autoinducer 2 import system permease protein |
| RA | 1,672,847 | A→G | 5.2% | A101A (GCT→GCC) | mdtI ← | multidrug efflux system transporter |
| RA | 1,685,802 | T→A | 5.1% | N263Y (AAC→TAC) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,685,853 | C→G | 6.8% | V246L (GTA→CTA) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,689,817 | C→A | 6.5% | intergenic (+66/‑35) | manA → / → ydgA | mannose‑6‑phosphate isomerase/DUF945 family protein |
| RA | 1,689,819 | A→T | 5.1% | intergenic (+68/‑33) | manA → / → ydgA | mannose‑6‑phosphate isomerase/DUF945 family protein |
| RA | 1,689,821 | T→G | 5.6% | intergenic (+70/‑31) | manA → / → ydgA | mannose‑6‑phosphate isomerase/DUF945 family protein |
| RA | 1,708,662 | C→G | 16.9% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,719,448 | C→T | 5.1% | C52Y (TGC→TAC) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,747,161 | C→A | 11.5% | P11T (CCT→ACT) | ydhS → | putative oxidoreductase |
| RA | 1,785,780 | T→C | 6.0% | K445E (AAA→GAA) | ppsA ← | phosphoenolpyruvate synthase |
| RA | 1,865,682 | G→C | 6.1% | intergenic (‑46/+44) | yeaE ← / ← mipA | aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery |
| RA | 1,928,799 | A→C | 5.0% | L14R (CTT→CGT) | ptrB ← | protease II |
| RA | 1,928,802 | G→T | 5.9% | T13K (ACG→AAG) | ptrB ← | protease II |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,027,173 | T→C | 5.4% | Y282C (TAT→TGT) | yedQ ← | putative membrane‑anchored diguanylate cyclase |
| RA | 2,130,410 | T→C | 5.5% | S157G (AGC→GGC) | wcaD ← | putative colanic acid polymerase |
| RA | 2,131,917 | A→T | 5.2% | Y52N (TAT→AAT) | wcaC ← | putative glycosyl transferase |
| RA | 2,147,351 | T→A | 5.1% | S64C (AGT→TGT) | alkA ← | 3‑methyl‑adenine DNA glycosylase II |
| RA | 2,147,360 | T→A | 5.3% | I61L (ATA→TTA) | alkA ← | 3‑methyl‑adenine DNA glycosylase II |
| 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 | 2,200,173 | C→T | 5.3% | pseudogene (852/948 nt) | yehH → | DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function |
| RA | 2,206,425 | T→A | 6.9% | V244E (GTG→GAG) | yehM → | uncharacterized protein |
| RA | 2,294,680 | Δ1 bp | 5.6% | coding (225/1944 nt) | ccmF ← | heme lyase, CcmF subunit |
| RA | 2,304,762 | T→C | 12.9% | intergenic (+369/+346) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,988 | T→C | 13.1% | intergenic (+595/+120) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,317,667 | T→G | 100% | E737A (GAA→GCA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,512,090 | G→A | 6.9% | A206V (GCG→GTG) | mntH ← | manganese/divalent cation transporter |
| RA | 2,519,386 | A→G | 5.5% | R429R (CGT→CGC) | gltX ← | glutamyl‑tRNA synthetase |
| RA | 2,548,713 | C→T | 5.3% | S204S (AGC→AGT) | yfeW → | penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity |
| RA | 2,599,194 | C→A | 5.3% | A189A (GCG→GCT) | dapA ← | dihydrodipicolinate synthase |
| RA | 2,609,406 | T→C | 5.9% | F307S (TTC→TCC) | hyfG → | hydrogenase 4, subunit |
| RA | 2,632,046 | G→T | 100% | P164T (CCG→ACG) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| RA | 2,653,367 | G→A | 6.9% | intergenic (+28/‑488) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,372 | T→C | 7.0% | intergenic (+33/‑483) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,818,145 | T→C | 19.1% | intergenic (‑10/+53) | argZ ← / ← argY | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,149 | T→C | 14.3% | intergenic (‑14/+49) | argZ ← / ← argY | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,158 | T→A | 13.7% | intergenic (‑23/+40) | argZ ← / ← argY | tRNA‑Arg/tRNA‑Arg |
| RA | 2,847,034 | C→T | 5.1% | A127T (GCG→ACG) | hycD ← | hydrogenase 3, membrane subunit |
| RA | 2,947,466 | T→C | 19.3% | intergenic (+3/‑31) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 3,002,530 | G→A | 100% | G729D (GGT→GAT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,107,875 | A→G | 5.8% | I427I (ATT→ATC) | speC ← | ornithine decarboxylase, constitutive |
| RA | 3,156,366 | G→A | 5.5% | G338S (GGC→AGC) | yqhD → | aldehyde reductase, NADPH‑dependent |
| RA | 3,176,313 | C→T | 5.0% | W174* (TGG→TAG) | cpdA ← | 3',5' cAMP phosphodiesterase |
| RA | 3,180,505 | G→T | 7.8% | E29* (GAG→TAG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,180,506 | A→C | 7.8% | E29A (GAG→GCG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,180,513:1 | +A | 5.9% | coding (93/1161 nt) | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,250,990 | A→T | 5.0% | intergenic (+36/‑34) | yqjF → / → yqjG | putative quinol oxidase subunit/putative S‑transferase |
| RA | 3,439,588 | G→C | 6.7% | intergenic (‑79/+28) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 6.9% | intergenic (‑80/+27) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| 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 | 3,781,131 | T→G | 5.4% | intergenic (+114/‑84) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,132 | C→G | 5.3% | intergenic (+115/‑83) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,138 | A→C | 6.2% | intergenic (+121/‑77) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,992,052 | T→A | 89.3% | D300E (GAT→GAA) | cyaA → | adenylate cyclase |
| RA | 4,060,261 | G→T | 6.4% | intergenic (+31/‑186) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,060,264 | A→C | 7.0% | intergenic (+34/‑183) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,153,420 | G→A | 7.3% | intergenic (‑322/+276) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,421 | C→A | 8.1% | intergenic (‑323/+275) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,427 | G→T | 5.6% | intergenic (‑329/+269) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,428 | A→C | 6.3% | intergenic (‑330/+268) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,434 | T→G | 7.9% | intergenic (‑336/+262) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,435 | T→C | 7.8% | intergenic (‑337/+261) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,227,550 | G→A | 7.0% | intergenic (+39/‑181) | metH → / → yjbB | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter |
| RA | 4,227,555 | A→T | 6.1% | intergenic (+44/‑176) | metH → / → yjbB | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter |
| RA | 4,227,560 | T→C | 6.1% | intergenic (+49/‑171) | metH → / → yjbB | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent/putative Na+/Pi‑cotransporter |
| RA | 4,296,060 | C→T | 38.2% | 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 | 4,378,757 | T→C | 5.1% | D63G (GAC→GGC) | ampC ← | penicillin‑binding protein; beta‑lactamase, intrinsically weak |
| RA | 4,454,592 | T→C | 5.0% | intergenic (+14/+19) | yjfF → / ← fbp | putative sugar ABC transporter permease/fructose‑1,6‑bisphosphatase I |
| RA | 4,454,593 | G→A | 5.0% | intergenic (+15/+18) | yjfF → / ← fbp | putative sugar ABC transporter permease/fructose‑1,6‑bisphosphatase I |
| RA | 4,606,239 | A→G | 46.3% | noncoding (48/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,613,051 | A→G | 5.2% | Y214C (TAC→TGC) | yjjU → | putative patatin‑like family phospholipase |
| RA | 4,619,906 | C→A | 93.0% | H102N (CAC→AAC) | deoB → | phosphopentomutase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423739–3424234 | 3424566–3424238 | 5–828 | 36 [31] | [31] 32 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3514372 | 3515089 | 718 | 32 [31] | [31] 35 | [gph]–[dam] | [gph],rpe,[dam] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 225154 = | NA (NA) | 5 (0.060) | 5/254 | NT | NA | noncoding (1384/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 225176 = | NA (NA) | noncoding (1406/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 750165 = | 90 (1.040) | 5 (0.060) | 3/250 | NT | 5.8% | coding (2005/2448 nt) | ybgQ | putative outer membrane protein |
| ? | NC_000913 | 750196 = | 77 (0.940) | coding (1974/2448 nt) | ybgQ | putative outer membrane protein | |||||
| * | ? | NC_000913 | 1207790 = | 45 (0.520) | 13 (0.170) | 12/232 | NT | 20.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 59 (0.770) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 45 (0.520) | 13 (0.170) | 12/232 | NT | 20.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 59 (0.770) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 110 (1.310) | 87/256 | 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 | |||||
| * | ? | NC_000913 | = 1666151 | 58 (0.670) | 3 (0.040) | 3/250 | NT | 5.2% | coding (837/1257 nt) | clcB | H(+)/Cl(‑) exchange transporter |
| ? | NC_000913 | = 1666184 | 55 (0.670) | coding (870/1257 nt) | clcB | H(+)/Cl(‑) exchange transporter | |||||
| * | ? | NC_000913 | 2149035 = | 60 (0.690) | 3 (0.040) | 3/248 | NT | 5.2% | intergenic (+9/+4) | yegD/yegI | Hsp70 chaperone family protein/protein kinase‑related putative non‑specific DNA‑binding protein |
| ? | NC_000913 | 2149074 = | 52 (0.640) | coding (1912/1947 nt) | yegI | protein kinase‑related putative non‑specific DNA‑binding protein | |||||