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 |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 730,791 | 0 | T | C | 53.8% | ‑4.1 / 27.0 | 26 | G403G (GGT→GGC) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 730,796 | 0 | G | C | 53.8% | 7.3 / 42.3 | 26 | G405A (GGC→GCC) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 2,939,148 | 0 | A | G | 37.5% | 12.6 / 22.7 | 24 | R87R (CGA→CGG) | fucU | L‑fucose mutarotase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 33.3% | 57.1 / 11.3 | 27 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 2,999,171 | 0 | A | G | 26.2% | 63.6 / 26.3 | 42 | Y241H (TAC→CAC) | ygeR | LysM domain‑containing putative peptidase lipoprotein YgeR |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.0% | 49.3 / 13.6 | 28 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,325,888 | 0 | G | T | 25.0% | 56.6 / 14.8 | 28 | intergenic (‑147/+511) | yjdN/yjdM | conserved protein YjdN/conserved protein YjdM |
| * | NC_000913 | 4,325,891 | 0 | T | C | 22.2% | 37.7 / 11.7 | 28 | intergenic (‑150/+508) | yjdN/yjdM | conserved protein YjdN/conserved protein YjdM |
| * | NC_000913 | 4,460,722 | 0 | A | G | 21.9% | 54.6 / 14.1 | 32 | C647R (TGT→CGT) | nrdD | anaerobic ribonucleoside‑triphosphate reductase |
| * | NC_000913 | 1,511,403 | 0 | G | A | 21.6% | 76.4 / 14.1 | 37 | R467R (CGG→CGA) | ydcR | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YdcR |
| * | NC_000913 | 2,243,025 | 0 | T | C | 21.4% | 71.4 / 20.2 | 42 | T210A (ACG→GCG) | folE | GTP cyclohydrolase 1 |
| * | NC_000913 | 1,427,803 | 0 | G | C | 20.8% | 135.8 / 30.1 | 48 | T308T (ACC→ACG) | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | NC_000913 | 1,427,783 | 0 | A | G | 20.0% | 105.0 / 20.5 | 50 | V315A (GTG→GCG) | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 608007 = | NA (NA) | 7 (0.270) | 5/224 | 2.3 | 15.6% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 38 (1.480) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 1207805 | 27 (0.850) | 5 (0.180) | 5/244 | 2.5 | 16.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 26 (0.930) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 34 (1.070) | 5 (0.170) | 5/258 | 2.6 | 12.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 39 (1.320) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2899597 | 46 (1.450) | 4 (0.140) | 4/256 | 3.0 | 8.2% | coding (677/786 nt) | ygcW | putative deoxygluconate dehydrogenase |
| ? | NC_000913 | = 2899686 | 47 (1.600) | coding (588/786 nt) | ygcW | putative deoxygluconate dehydrogenase | |||||
| * | ? | NC_000913 | = 4498064 | 1 (0.030) | 5 (0.160) | 4/276 | 3.1 | 83.3% | intergenic (+124/‑208) | intB/insC‑6 | KpLE2 phage‑like element; putative integrase/KpLE2 phage‑like element; IS2 insertion element repressor InsA |
| ? | NC_000913 | = 4519239 | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 4628780 | NA (NA) | 3 (0.110) | 3/240 | 3.2 | NA | noncoding (37/37 nt) | other | REP354b |
| ? | NC_000913 | = 4633089 | NA (NA) | intergenic (+3/+144) | trpR/yjjX | DNA‑binding transcriptional repressor TrpR/ITPase/XTPase | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 3 (0.110) +GAACGCCTTATCCGGT |
3/244 | 3.2 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 899694 | NA (NA) | 3 (0.110) | 3/248 | 3.3 | NA | intergenic (+49/+150) | rlmC/artJ | 23S rRNA m(5)U747 methyltransferase/L‑arginine ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 900783 | NA (NA) | noncoding (1/34 nt) | other | REP83a | |||||
| * | ? | NC_000913 | 377321 = | NA (NA) | 4 (0.130) | 3/268 | 3.5 | NA | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | = 508817 | NA (NA) | noncoding (2/34 nt) | other | REP48e | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 4 (0.130) +T |
3/274 | 3.5 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||