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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 264,098 | G→T | 100% | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 275,065 | G→A | 100% | T18I (ACC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 389,919:1 | +T | 100% | intergenic (‑192/‑332) | hemB ← / → yaiT | 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 482,230 | G→A | 100% | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 550,955 | C→T | 9.0% | L173F (CTC→TTC) | ybcF → | putative carbonate kinase |
| RA | 1,158,559 | C→T | 100% | Q231* (CAG→TAG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,196,232 | C→T | 20.2% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,197,502 | C→T | 100% | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,224,239 | A→T | 11.5% | intergenic (+332/+40) | ycgI → / ← minE | pseudogene/cell division topological specificity factor |
| RA | 1,544,022 | 1 bp→AA | 100% | coding (39/1389 nt) | narU ← | nitrate/nitrite transporter |
| RA | 1,726,165 | A→G | 43.6% | Y48C (TAC→TGC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| JC | 1,726,433 | Δ11 bp | 33.3% | coding (411‑421/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,530 | G→C | 29.1% | A170P (GCG→CCG) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,734,464 | G→C | 20.3% | T10T (ACG→ACC) | mepH → | murein DD‑endopeptidase, space‑maker hydrolase |
| RA | 1,774,576 | G→A | 100% | G263E (GGG→GAG) | ydiB → | quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,106,741 | A→T | 100% | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| 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 | 2,679,525 | G→T | 100% | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,795,396 | C→A | 100% | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,817,170 | C→A | 100% | E112* (GAA→TAA) | yqaB ← | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| RA | 2,948,287 | T→C | 9.8% | I242V (ATC→GTC) | amiC ← | N‑acetylmuramoyl‑L‑alanine amidase |
| RA | 2,948,288 | G→A | 8.4% | D241D (GAC→GAT) | amiC ← | N‑acetylmuramoyl‑L‑alanine amidase |
| RA | 2,976,638 | T→G | 69.2% | S14A (TCA→GCA) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 2,976,684 | G→T | 19.0% | S29I (AGC→ATC) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| 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 | 4,183,136 | G→T | 72.8% | R637L (CGT→CTT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,187,572 | G→T | 18.9% | M747I (ATG→ATT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,042 | C→T | 16.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,362:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,604,698 | C→A | 100% | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_hsa_tpiA | 365890 | 366373 | 484 | 10 [8] | [8] 9 | [lacZ] | [lacZ] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | 129734 = | 46 (1.320) | 3 (0.090) | 3/264 | NT | 6.3% | coding (1527/1854 nt) | yacH | DUF3300 family protein |
| ? | NC_000913_3_hsa_tpiA | 129754 = | 45 (1.350) | coding (1507/1854 nt) | yacH | DUF3300 family protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 357155 | 39 (1.120) | 3 (0.090) | 3/264 | NT | 7.4% | coding (985/1284 nt) | codA | cytosine/isoguanine deaminase |
| ? | NC_000913_3_hsa_tpiA | = 357165 | 38 (1.140) | coding (995/1284 nt) | codA | cytosine/isoguanine deaminase | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1207790 = | 7 (0.200) | 16 (0.520) | 15/244 | NT | 66.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | 1209619 = | 10 (0.330) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1207805 | 9 (0.260) | 22 (0.720) | 20/244 | NT | 71.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | = 1209602 | 10 (0.330) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1299498 | 0 (0.000) | 48 (1.420) | 38/268 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_hsa_tpiA | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||