mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 199,121 | C→T | V398V (GTC→GTT) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 315,061 | G→T | pseudogene (705/872 nt) | eaeH → | pseudogene, attaching and effacing protein homology,factor, Not classified |
| RA | 456,497 | (T)8→7 | intergenic (+66/‑180) | tig → / → clpP | peptidyl‑prolyl cis/trans isomerase (trigger factor)/proteolytic subunit of ClpA‑ClpP and ClpX‑ClpP ATP‑dependent serine proteases |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 630,819 | C→T | A309V (GCG→GTG) | cstA → | carbon starvation protein involved in peptide utilization, APC peptide transporter family protein |
| RA | 1,042,246 | A→G | S655S (AGT→AGC) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,240,435 | T→C | Q546R (CAG→CGG) | cvrA ← | putative cation/proton antiporter |
| RA | 1,245,903 | (T)5→4 | coding (1474/1698 nt) | treA ← | periplasmic trehalase |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,339,927 | A→G | S200G (AGC→GGC) | pgpB → | phosphatidylglycerophosphatase B |
| RA | 1,350,817 | A→G | F75L (TTC→CTC) | fabI ← | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent |
| RA | 1,426,252 | A→G | intergenic (+170/‑202) | ydaY → / → tmpR | pseudogene, Rac prophage,Phage or Prophage Related/Rac prophage, pseudogene, tail protein family,Phage or Prophage Related, putative alpha helix protein |
| RA | 1,437,231 | (T)9→8 | intergenic (+2/+29) | micC → / ← pfo | sRNA antisense regulator of OmpC translation, Hfq‑dependent/pyruvate‑flavodoxin oxidoreductase |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,467,061 | C→T | pseudogene (1670/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,629,489 | G→A | G475G (GGC→GGT) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,635,023 | T→C | A275A (GCA→GCG) | stfQ ← | Qin prophage, putative side tail fibre assembly protein |
| RA | 1,635,026 | A→G | H274H (CAT→CAC) | stfQ ← | Qin prophage, putative side tail fibre assembly protein |
| RA | 1,635,029 | C→T | A273A (GCG→GCA) | stfQ ← | Qin prophage, putative side tail fibre assembly protein |
| RA | 1,635,032 | G→A | G272G (GGC→GGT) | stfQ ← | Qin prophage, putative side tail fibre assembly protein |
| RA | 1,635,059 | C→T | S263S (TCG→TCA) | stfQ ← | Qin prophage, putative side tail fibre assembly protein |
| RA | 1,756,216 | (A)5→4 | coding (519/1413 nt) | pykF → | pyruvate kinase I |
| RA | 1,818,550 | (C)7→8 | intergenic (‑50/+55) | chbF ← / ← chbR | phospho‑chitobiase, general 6‑phospho‑beta‑glucosidase activity/repressor of chb operon for N,N'‑diacetylchitobiose utilization |
| RA | 1,827,934 | G→A | A109V (GCC→GTC) | astB ← | succinylarginine dihydrolase |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,941,430 | G→A | P69L (CCG→CTG) | mepM ← | murein DD‑endopeptidase, space‑maker hydrolase, septation protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,036,909 | T→C | Q415R (CAG→CGG) | yedV ← | putative sensory kinase in two‑component regulatory system with YedW |
| RA | 2,052,156 | C→T | intergenic (+142/+120) | yeeJ → / ← yeeL | putative adhesin/pseudogene, glycosyltransferase homology |
| RA | 2,102,890 | T→C | R8G (AGA→GGA) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC |
| RA | 2,250,649 | C→T | H311H (CAC→CAT) | yeiH → | UPF0324 family inner membrane protein |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,435,114 | A→G | W175R (TGG→CGG) | truA ← | tRNA pseudouridine(38‑40) synthase |
| RA | 2,459,283 | G→A | A396V (GCG→GTG) | fadI ← | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit |
| RA | 2,546,932 | C→T | P87L (CCG→CTG) | murP → | N‑acetylmuramic acid permease, EIIBC component, PTS system |
| RA | 2,720,122 | T→C | V57A (GTG→GCG) | pka → | protein lysine acetyltransferase |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,920,310 | A→G | V146A (GTC→GCC) | gudX ← | glucarate dehydratase‑related protein, substrate unknown |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 2,965,748 | T→C | D97G (GAC→GGC) | lgt ← | phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase |
| RA | 2,968,260 | (T)6→5 | coding (175/2247 nt) | ptsP ← | PEP‑protein phosphotransferase enzyme I, GAF domain containing protein |
| RA | 3,067,677 | G→A | A135V (GCG→GTG) | yggE ← | oxidative stress defense protein |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,284,931 | A→G | T83A (ACC→GCC) | agaC → | N‑acetylgalactosamine‑specific enzyme IIC component of PTS |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,560,455 | +G | 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 | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,868,399 | C→T | C304Y (TGT→TAT) | yidR ← | DUF3748 family protein |
| RA | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 3,950,476 | (T)8→7 | intergenic (+56/‑31) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| RA | 3,975,924 | T→C | L260P (CTG→CCG) | wecE → | TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase |
| RA | 4,185,540 | C→T | P64L (CCG→CTG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,533,530 | C→T | L85L (CTG→CTA) | yjhQ ← | GNAT family putative N‑acetyltransferase |
| RA | 4,538,491 | C→T | G92D (GGC→GAC) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,627,489 | T→C | F59L (TTT→CTT) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| RA | 4,635,400 | (T)7→6 | intergenic (‑90/‑121) | rob ← / → creA | right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 807327 | 810368 | 3042 | 11 [9] | [10] 11 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1633071–1633221 | 1634978–1634645 | 1425–1908 | 14 [9] | [9] 14 | ydfK–[stfQ] | ydfK, pinQ, tfaQ, [stfQ] |
| * | * | ÷ | NC_000913 | 2857130 | 2859625 | 2496 | 12 [9] | [10] 11 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423755–3424234 | 3424540–3424238 | 5–786 | 11 [7] | [10] 12 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 14 (0.260) | 67 (1.460) | 39/198 | 0.1 | 89.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 4 (0.090) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 14 (0.260) | 38 (0.830) | 26/198 | 0.6 | 82.6% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 4 (0.090) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 60 (1.170) | 43/222 | 0.1 | 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 | |||||