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 | ||
| * | CP009273 | 3,774,404 | 0 | T | A | 34.3% | 366.5 / 46.7 | 182 | intergenic (+27/‑171) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | CP009273 | 910,655 | 0 | A | T | 29.3% | 525.4 / 54.0 | 251 | intergenic (‑342/+153) | ybjE/aqpZ | putative transporter/aquaporin Z |
| * | CP009273 | 2,222,683 | 0 | T | A | 28.6% | 457.5 / 56.3 | 216 | intergenic (+139/+234) | yohP/dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| * | CP009273 | 3,774,398 | 0 | T | A | 26.9% | 417.3 / 27.1 | 191 | intergenic (+21/‑177) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | CP009273 | 2,222,692 | 0 | G | C | 25.4% | 492.3 / 90.0 | 213 | intergenic (+148/+225) | yohP/dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| * | CP009273 | 910,669 | 0 | A | T | 25.0% | 533.7 / 39.9 | 247 | intergenic (‑356/+139) | ybjE/aqpZ | putative transporter/aquaporin Z |
| * | CP009273 | 3,952,834 | 0 | T | A | 24.2% | 688.1 / 32.0 | 267 | intergenic (+29/+58) | ilvC/ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| * | CP009273 | 3,774,410 | 0 | T | A | 23.8% | 443.4 / 17.8 | 179 | intergenic (+33/‑165) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | CP009273 | 2,222,669 | 0 | T | A | 22.4% | 567.9 / 51.9 | 233 | intergenic (+125/+248) | yohP/dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| * | CP009273 | 910,646 | 0 | C | G | 22.0% | 605.7 / 89.0 | 245 | intergenic (‑333/+162) | ybjE/aqpZ | putative transporter/aquaporin Z |
| * | CP009273 | 161,100 | 0 | T | A | 20.6% | 505.1 / 23.9 | 173 | intergenic (+79/‑117) | hrpB/mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| * | CP009273 | 3,774,392 | 0 | T | A | 20.5% | 455.6 / 13.2 | 200 | intergenic (+15/‑183) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 4532507 | 269 (0.900) | 60 (0.210) | 45/280 | 17.2 | 19.4% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 247 (0.880) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | 4532499 = | 258 (0.860) | 56 (0.200) | 43/280 | 18.0 | 18.5% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 251 (0.890) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 2514718 | 237 (0.790) | 4 (0.020) | 4/200 | 33.6 | 2.5% | noncoding (446/1345 nt) | IS186 | repeat region |
| ? | CP009273 | 2514875 = | NA (NA) | noncoding (603/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | = 2811301 | 262 (0.870) | 16 (0.060) | 10/258 | 33.7 | 6.6% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | CP009273 | 2811851 = | 228 (0.880) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | CP009273 | = 2811716 | 252 (0.840) | 16 (0.060) | 9/258 | 34.5 | 6.7% | intergenic (‑83/+116) | argY/argV | tRNA‑Arg/tRNA‑Arg |
| ? | CP009273 | 2811851 = | 228 (0.880) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | CP009273 | 1406156 = | 280 (0.930) | 7 (0.030) | 6/246 | 36.2 | 2.8% | coding (50/936 nt) | ttcA | tRNA 2‑thiocytidine biosynthesis protein |
| ? | CP009273 | = 1429215 | 260 (1.050) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 776902 | 201 (0.670) | 10 (0.040) | 7/258 | 36.4 | 5.0% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | CP009273 | 2514846 = | 207 (0.800) | noncoding (574/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | = 587010 | 305 (1.020) | 3 (0.010) | 3/272 | 41.9 | 1.1% | coding (1625/2238 nt) | nfrB | bacteriophage N4 receptor, inner membrane subunit |
| ? | CP009273 | 587236 = | 277 (1.010) | coding (1399/2238 nt) | nfrB | bacteriophage N4 receptor, inner membrane subunit | |||||
| * | ? | CP009273 | = 361823 | 230 (0.770) | 3 (0.010) +TTAATTAA |
3/282 | 42.8 | 1.2% | coding (831/834 nt) | mhpR | mhp operon transcriptional activator |
| ? | CP009273 | 4033991 = | 293 (0.980) | noncoding (115/120 nt) | rrfA | 5S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | = 2351352 | 256 (0.850) | 4 (0.010) | 4/298 | 42.9 | 1.5% | coding (58/186 nt) | ypaA | uncharacterized protein |
| ? | CP009273 | 2351365 = | 253 (0.840) | coding (71/186 nt) | ypaA | uncharacterized protein | |||||