mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 14,266 | C→A | H33Q (CAC→CAA) | dnaJ → | chaperone protein DnaJ |
| RA | 81,102 | G→A | S286L (TCG→TTG) | leuB ← | 3‑isopropylmalate dehydrogenase |
| RA | 156,068 | A→G | V45A (GTA→GCA) | yadV ← | putative fimbrial chaperone YadV |
| RA | 156,591 | T→C | K98R (AAA→AGA) | yadN ← | putative fimbrial protein YadN |
| RA | 167,798 | C→A | Y105* (TAC→TAA) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 229,552 | C→T | S129F (TCC→TTC) | dkgB → | methylglyoxal reductase DkgB |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 363,261 | G→T | Y1015* (TAC→TAA) | lacZ ← | beta‑galactosidase |
| RA | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 789,580 | C→A | E134* (GAA→TAA) | galK ← | galactokinase |
| RA | 1,001,251 | A→C | Q679P (CAA→CCA) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,125,694 | Δ1 bp | coding (133/585 nt) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | 1,143,323 | C→T | D349N (GAC→AAC) | rne ← | ribonuclease E |
| JC JC | 1,144,921 | IS5 (+) +4 bp | intergenic (+99/‑16) | yceQ → / → rluC | DUF2655 domain‑containing protein YceQ/23S rRNA pseudouridine(955/2504/2580) synthase |
| RA | 1,148,972 | C→T | Q72* (CAG→TAG) | fabH → | 3‑oxoacyl‑[acyl carrier protein] synthase 3 |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,287,040 | G→A | intergenic (+56/+26) | ychS → / ← rttR | putative uncharacterized protein YchS/small RNA RttR |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,336,674 | G→A | G282R (GGG→AGG) | acnA → | aconitate hydratase 1 |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,339,315 | C→T | intergenic (‑155/‑15) | ribA ← / → pgpB | GTP cyclohydrolase 2/phosphatidylglycerophosphatase B |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| MC JC | 1,397,239 | Δ2,351 bp | IS5‑mediated | ynaJ–fnr | ynaJ, uspE, fnr |
| RA | 1,600,222 | G→T | intergenic (‑13/+66) | lsrK ← / ← lsrR | autoinducer‑2 kinase/DNA‑binding transcriptional repressor LsrR |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,656,656 | IS2 (–) +5 bp | coding (473‑477/561 nt) | speG → | spermidine N‑acetyltransferase |
| RA | 1,829,887 | G→A | A293A (GCC→GCT) | astA ← | arginine N‑succinyltransferase |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| JC JC | 1,937,701 | IS2 (+) +5 bp | coding (53‑57/1443 nt) | pykA → | pyruvate kinase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,042,171 | G→A | intergenic (+146/‑197) | zinT → / → yodB | metal‑binding protein ZinT/putative cytochrome b561 YodB |
| RA | 2,044,642 | T→C | intergenic (+18/‑296) | asnT → / → yeeJ | tRNA‑Asn/inverse autotransporter adhesin |
| RA | 2,111,259 | Δ1 bp | coding (718/900 nt) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,173,448 | C→T | intergenic (‑575/+834) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,176,491 | IS1 (+) +9 bp | coding (706‑714/855 nt) | gatY ← | tagatose‑1,6‑bisphosphate aldolase 2 |
| RA | 2,245,221 | C→G | V517L (GTA→CTA) | cirA ← | iron‑catecholate outer membrane transporter CirA |
| JC JC | 2,468,298 | IS3 (+) +3 bp | coding (85‑87/921 nt) | yfdH → | bactoprenol glucosyl transferase |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| RA | 2,726,177 | G→T | noncoding (12/120 nt) | rrfG ← | 5S ribosomal RNA |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 3,100,161 | C→G | V190L (GTA→CTA) | ansB ← | L‑asparaginase 2 |
| RA | 3,152,494 | G→T | A87S (GCG→TCG) | metC → | cystathionine beta‑lyase/L‑cysteine desulfhydrase/alanine racemase |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,329,743 | G→T | D261Y (GAT→TAT) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| JC JC | 3,350,556 | IS1 (–) +8 bp | intergenic (‑97/‑14) | elbB ← / → arcZ | low activity glyoxalase ElbB/small regulatory RNA ArcZ |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| JC JC | 3,429,986 | IS3 (–) +5 bp :: +T | coding (34‑38/258 nt) | yrdB ← | DUF1488 domain‑containing protein YrdB |
| RA | 3,560,443 | C→G | intergenic (+577/+179) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,707,883 | G→A | intergenic (‑178/+733) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| JC JC | 4,123,934 | IS1 (+) +9 bp | coding (515‑523/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,212,973 | Δ1 bp | intergenic (+27/‑67) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,287,464 | T→A | intergenic (‑93/‑147) | acs ← / → ytcB | acetyl‑CoA synthetase (AMP‑forming)/protein YtcB |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,473,900 | C→T | G52R (GGA→AGA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,475,493 | T→C | F19F (TTT→TTC) | yjgL → | protein YjgL |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| JC JC | 4,542,042 | IS1 (+) +8 bp | coding (6‑13/597 nt) | fimE → | regulator for fimA |
| RA | 4,563,778 | (G)6→5 | coding (148/258 nt) | ytiA ← | uncharacterized protein YtiA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2558699 | 2565482 | 6784 | 50 [0] | [3] 6 | intZ–[eutA] | intZ,yffL,yffM,yffN,yffO,yffP,yffQ,yffR,yffS,[eutA] |
| * | * | ÷ | NC_000913 | 4035400–4036859 | 4036859 | 1–1460 | 4 [3] | [3] 4 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 47 (1.130) | 45/484 | 0.1 | 55.3% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 258921 = | 38 (0.920) | pseudogene (246/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 39 (0.940) | 34/484 | 0.3 | 47.6% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 323450 | 43 (1.040) | coding (1113/1428 nt) | ykgF | putative amino acid dehydrogenase with NAD(P)‑binding domain and ferridoxin‑like domain | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 43 (1.040) | 41/484 | 0.2 | 53.8% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 258929 | 37 (0.890) | pseudogene (254/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 45 (1.080) | 44/484 | 0.1 | 57.7% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 362204 = | 33 (0.790) | coding (976/1254 nt) | lacY | lactose permease | |||||
| * | ? | NC_000913 | 1207790 = | 30 (0.720) | 6 (0.150) | 6/452 | 2.6 | 20.7% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 18 (0.460) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 32 (0.770) | 7 (0.180) | 7/452 | 2.4 | 22.6% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 18 (0.460) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 2558698 | 0 (0.000) | 50 (1.250) | 47/468 | 0.1 | 100% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase subunit alpha/putative phage integrase IntZ |
| ? | NC_000913 | 2565489 = | 0 (0.000) | coding (1396/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA | |||||
| * | ? | NC_000913 | 4542682 = | 10 (0.240) | 21 (0.530) | 19/466 | 0.9 | 70.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 8 (0.200) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 9 (0.220) | 8 (0.200) | 8/466 | 2.2 | 49.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 8 (0.200) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||