mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 30 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,857,144 | 0 | C | T | 66.7% | 12.1 / 30.8 | 25 | L18F (CTC→TTC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,142 | 0 | A | G | 64.0% | 19.3 / 18.1 | 25 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 64.0% | 16.5 / 26.8 | 25 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,145 | 0 | T | A | 64.0% | 21.3 / 26.8 | 25 | L18H (CTC→CAC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,146 | 0 | C | G | 64.0% | 22.6 / 31.4 | 25 | L18L (CTC→CTG) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | T | 64.0% | 47.1 / 27.6 | 25 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | C | 64.0% | 50.2 / 28.8 | 25 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 1,286,965 | 0 | A | G | 58.0% | 16.8 / 82.3 | 81 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 566,205 | 0 | T | C | 52.8% | 30.2 / 107.5 | 89 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,245 | 0 | G | A | 52.8% | ‑4.3 / 101.8 | 72 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,173 | 0 | C | G | 52.0% | 10.7 / 190.0 | 102 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 1,287,143 | 0 | G | A | 50.0% | ‑0.5 / 20.5 | 16 | noncoding (94/171 nt) P12S (CCA→TCA) | rttR tpr | rtT sRNA, processed from tyrT transcript protamine‑like protein |
| * | NC_000913 | 566,277 | 0 | C | T | 47.6% | 25.6 / 100.8 | 82 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 4,518,992 | 0 | C | . | 42.1% | 152.9 / 118.9 | 76 | pseudogene (272/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 566,332 | 0 | T | G | 40.9% | 31.7 / 111.0 | 66 | pseudogene (45/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,323 | 0 | C | T | 40.3% | 54.7 / 65.8 | 67 | pseudogene (54/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,326 | 0 | T | C | 39.1% | 30.7 / 77.2 | 69 | pseudogene (51/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 4,518,963 | 0 | C | G | 38.5% | 98.1 / 77.0 | 52 | pseudogene (243/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 4,518,966 | 0 | A | G | 38.5% | 56.1 / 55.9 | 52 | pseudogene (246/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 2,857,141 | 1 | . | G | 36.0% | 16.3 / 37.4 | 25 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 67 (1.230) | 8 (0.170) | 8/174 | 2.9 | 14.6% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 37 (0.810) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 967030 = | 71 (1.310) | 3 (0.060) | 3/186 | 4.8 | 4.4% | coding (410/1749 nt) | msbA | lipid ABC transporter permease/ATPase |
| ? | NC_000913 | = 967026 | 67 (1.370) | coding (406/1749 nt) | msbA | lipid ABC transporter permease/ATPase | |||||
| * | ? | NC_000913 | = 2375831 | 40 (0.740) | 4 (0.070) | 3/204 | 5.1 | 8.2% | coding (132/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | 2375836 = | 50 (0.930) | coding (127/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase | |||||