mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 120,158:1 | +A | 6.0% | intergenic (+23/+20) | ampE → / ← aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| RA | 227,054 | G→A | 8.1% | noncoding (1296/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 483,017 | T→A | 5.6% | T463S (ACT→TCT) | acrB ← | multidrug efflux system protein |
| RA | 517,379 | C→A | 5.6% | intergenic (+17/+46) | fetB → / ← ybbN | iron export ABC transporter permease; peroxide resistance protein/DnaK co‑chaperone, thioredoxin‑like protein |
| RA | 517,380 | A→T | 6.6% | intergenic (+18/+45) | fetB → / ← ybbN | iron export ABC transporter permease; peroxide resistance protein/DnaK co‑chaperone, thioredoxin‑like protein |
| RA | 517,383 | A→T | 5.4% | intergenic (+21/+42) | fetB → / ← ybbN | iron export ABC transporter permease; peroxide resistance protein/DnaK co‑chaperone, thioredoxin‑like protein |
| RA | 580,115 | C→T | 5.8% | intergenic (+29/+136) | ybcW → / ← ylcI | DLP12 prophage; uncharacterized protein/DUF3950 family protein, DLP12 prophage |
| RA | 580,119 | A→G | 5.7% | intergenic (+33/+132) | ybcW → / ← ylcI | DLP12 prophage; uncharacterized protein/DUF3950 family protein, DLP12 prophage |
| RA | 580,120 | C→T | 5.7% | intergenic (+34/+131) | ybcW → / ← ylcI | DLP12 prophage; uncharacterized protein/DUF3950 family protein, DLP12 prophage |
| RA | 635,984 | C→T | 5.1% | A196T (GCA→ACA) | ybdN ← | PAPS reductase‑like domain protein |
| RA | 696,793 | T→A | 7.1% | noncoding (38/75 nt) | glnW ← | tRNA‑Gln |
| RA | 1,008,174 | A→T | 5.1% | K111* (AAA→TAA) | rlmL → | 23S rRNA m(2)G2445 and m(7)G2069 methyltransferases, SAM‑dependent |
| RA | 1,154,926 | A→T | 5.8% | N272I (AAC→ATC) | yceG → | septation protein, ampicillin sensitivity |
| JC JC | 1,335,761 | IS3 (–) +3 bp :: +TCA | 100% | intergenic (+303/‑68) | yciX → / → acnA | uncharacterized protein/aconitate hydratase 1; aconitase A |
| RA | 1,633,139 | A→G | 7.7% | D23G (GAT→GGT) | ydfK → | cold shock protein, function unknown, Qin prophage |
| RA | 1,636,068 | T→C | 6.1% | pseudogene (300/528 nt) | nohQ ← | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| RA | 1,636,074 | C→T | 5.5% | pseudogene (294/528 nt) | nohQ ← | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| RA | 1,662,350 | C→T | 100% | P599S (CCC→TCC) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,708,758 | G→C | 26.0% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,919,585 | T→A | 5.5% | G692G (GGT→GGA) | yebT → | MCE domain protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 2,304,649 | C→T | 12.9% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,691,169 | A→T | 5.0% | noncoding (172/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,691,173 | A→T | 5.1% | noncoding (168/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,722,608 | T→C | 5.1% | S886P (TCA→CCA) | pka → | protein lysine acetyltransferase |
| RA | 2,804,531 | G→T | 11.5% | intergenic (+70/‑284) | nrdF → / → proV | ribonucleoside‑diphosphate reductase 2, beta subunit, ferritin‑like protein/glycine betaine/proline ABC transporter periplasmic binding protein |
| RA | 2,810,872 | C→T | 5.7% | H35Y (CAC→TAC) ‡ | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 2,810,873 | A→G | 5.7% | H35R (CAC→CGC) ‡ | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 3,020,511 | C→G | 5.0% | intergenic (+22/‑29) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,156,590 | C→A | 5.7% | intergenic (+72/‑33) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,156,591 | T→G | 5.7% | intergenic (+73/‑32) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,234,506 | G→A | 5.1% | intergenic (‑51/+233) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,234,508 | T→C | 5.3% | intergenic (‑53/+231) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,269,968 | G→T | 7.9% | intergenic (+366/+248) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,269,969 | A→C | 6.4% | intergenic (+367/+247) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,269,970 | A→G | 7.5% | intergenic (+368/+246) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| 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 | 3,708,427 | G→A | 5.8% | intergenic (‑722/+189) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,428 | T→A | 5.2% | intergenic (‑723/+188) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,429 | T→C | 6.1% | intergenic (‑724/+187) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,815,809 | Δ1 bp | 10.7% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| JC | 3,815,859 | Δ82 bp | 9.3% | [rph]–[rph] | [rph], [rph] | |
| RA | 4,175,146 | Δ1 bp | 100% | intergenic (‑120/‑242) | coaA ← / → thrU | pantothenate kinase/tRNA‑Thr |
| RA | 4,182,820 | C→T | 62.7% | H526Y (CAC→TAC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,187,524 | G→T | 12.2% | M725I (ATG→ATT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,060 | C→T | 29.1% | 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 131569 | 134213 | 2645 | 50 [48] | [47] 49 | acnB | acnB |
| * | * | ÷ | NC_000913 | 3423731–3424234 | 3424580–3424239 | 6–850 | 49 [48] | [48] 50 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 275044 | NA (NA) | 4 (0.030) | 4/246 | NT | NA | noncoding (106/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 275058 | NA (NA) | noncoding (92/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 27 (0.230) | 67 (0.660) | 54/218 | NT | 66.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 44 (0.430) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 26 (0.220) | 48 (0.470) | 37/218 | NT | 59.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 44 (0.430) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 148 (1.310) | 106/242 | 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 | = 1335074 | 10 (0.090) | 133 (1.140) | 85/250 | NT | 95.7% | intergenic (+245/‑50) | cysB/ymiA | N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor/uncharacterized protein |
| ? | NC_000913 | 1335789 = | 2 (0.020) | intergenic (+331/‑42) | yciX/acnA | uncharacterized protein/aconitate hydratase 1; aconitase A | |||||
| * | ? | NC_000913 | = 2690411 | 96 (0.820) | 5 (0.050) | 5/234 | NT | 5.1% | coding (688/1428 nt) | glrK | sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| ? | NC_000913 | = 2690416 | 95 (0.870) | coding (683/1428 nt) | glrK | sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR | |||||
| * | ? | NC_000913 | = 4209893 | 14 (0.120) | 4 (0.040) | 4/228 | NT | 23.9% | intergenic (+44/‑150) | gltV/rrlE | tRNA‑Glu/23S ribosomal RNA of rrnE operon |
| ? | NC_000913 | = 4209911 | NA (NA) | intergenic (+62/‑132) | gltV/rrlE | tRNA‑Glu/23S ribosomal RNA of rrnE operon | |||||
| * | ? | NC_000913 | 4542682 = | 123 (1.050) | 27 (0.250) | 25/232 | NT | 18.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 131 (1.210) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 121 (1.040) | 22 (0.200) | 20/232 | NT | 15.3% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 131 (1.210) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||