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 | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 1,662,350 | C→T | P599S (CCC→TCC) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,806,340 | C→T | intergenic (‑257/‑30) | ydiY ← / → pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| 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 | 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 |
| JC JC | 3,560,930 | IS5 (+) +4 bp | coding (520‑523/831 nt) | glpG ← | rhomboid intramembrane serine protease |
| RA | 4,182,881 | A→C | E546A (GAA→GCA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | 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 | 2185834 | 2185861 | 28 | 6 [4] | [4] 6 | rcnR/rcnA | transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance |
| * | * | ÷ | NC_000913 | 3423751–3424234 | 3424549–3424238 | 5–799 | 5 [4] | [3] 5 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4107528 | 4108498 | 971 | 6 [4] | [3] 5 | [pfkA] | [pfkA] |
| * | * | ÷ | NC_000913 | 4144055 | 4147087 | 3033 | 6 [1] | [4] 6 | [pflD]–[pflC] | [pflD],[pflC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 224374 | NA (NA) | 4 (0.150) | 4/252 | 3.0 | NA | noncoding (604/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 224403 | NA (NA) | noncoding (633/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 271191 | NA (NA) | 6 (0.230) | 4/254 | 3.0 | NA | noncoding (651/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 271214 | NA (NA) | noncoding (674/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 282890 | 20 (0.720) | 6 (0.220) | 5/260 | 2.7 | 21.6% | coding (613/909 nt) | yagE | 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| ? | NC_000913 | = 282923 | 24 (0.880) | coding (646/909 nt) | yagE | 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage | |||||
| * | ? | NC_000913 | 715247 = | NA (NA) | 4 (0.150) +CAGTCTCA |
4/250 | 2.9 | NA | intergenic (+49/‑165) | pgm/ybfP | phosphoglucomutase/lipoprotein |
| ? | NC_000913 | = 3012605 | NA (NA) | intergenic (+212/+9) | yqeA/yqeB | putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold | |||||
| * | ? | NC_000913 | 1207790 = | 32 (1.150) | 8 (0.330) | 8/234 | 1.7 | 27.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 14 (0.570) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 26 (0.970) | 26/258 | 0.2 | 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 | = 4524799 | 19 (0.680) | 4 (0.160) | 4/246 | 2.9 | 20.2% | coding (212/906 nt) | yjhH | putative lyase/synthase |
| ? | NC_000913 | = 4524824 | 14 (0.550) | coding (187/906 nt) | yjhH | putative lyase/synthase | |||||