mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 27 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,857,141 | 1 | . | G | 61.1% | 114.0 / 72.3 | 54 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | . | 61.1% | 17.1 / 98.2 | 54 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | . | 61.1% | 29.5 / 91.9 | 54 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,144 | 0 | C | G | 55.3% | 53.6 / 63.3 | 54 | L18V (CTC→GTC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 4,171,557 | 0 | C | A | 55.2% | 5.6 / 53.1 | 29 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| * | NC_000913 | 566,205 | 0 | T | C | 50.4% | 23.0 / 161.4 | 125 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,173 | 0 | C | G | 50.0% | ‑1.1 / 249.8 | 130 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,143 | 1 | . | A | 48.1% | 86.0 / 129.7 | 54 | coding (51/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 1,286,965 | 0 | A | G | 46.8% | 36.6 / 126.8 | 94 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 1,097,392 | 1 | . | G | 45.5% | 4.9 / 18.6 | 11 | intergenic (+563/+173) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| * | NC_000913 | 566,245 | 0 | G | A | 43.0% | 77.6 / 133.1 | 121 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,277 | 0 | C | T | 41.8% | 93.5 / 144.4 | 134 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 4,518,992 | 0 | C | . | 40.2% | 227.4 / 156.7 | 107 | pseudogene (272/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 2,857,142 | 0 | A | G | 38.9% | 32.1 / 52.3 | 54 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 38.9% | 53.7 / 62.6 | 54 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,145 | 0 | T | A | 38.9% | 55.3 / 61.0 | 54 | L18H (CTC→CAC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,146 | 0 | C | G | 38.9% | 59.7 / 72.7 | 54 | L18L (CTC→CTG) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,323 | 0 | C | T | 34.8% | 134.0 / 95.5 | 112 | pseudogene (54/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,326 | 0 | T | C | 34.2% | 98.0 / 108.0 | 114 | pseudogene (51/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,332 | 0 | T | G | 33.9% | 126.9 / 151.8 | 109 | pseudogene (45/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| 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 | = 4038562 | NA (NA) | 4 (0.060) | 4/198 | 6.2 | 100% | noncoding (1044/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon |
| ? | NC_000913 | 4038567 = | 0 (0.000) | noncoding (1049/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | = 226805 | NA (NA) | 4 (0.060) | 4/198 | 6.2 | NA | noncoding (1047/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 226810 = | NA (NA) | noncoding (1052/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 3818583 | 46 (0.690) | 5 (0.080) | 3/202 | 6.8 | 9.3% | coding (824/825 nt) | dinD | DNA damage‑inducible protein |
| ? | NC_000913 | 3818590 = | 52 (0.780) | intergenic (+6/‑284) | dinD/yicG | DNA damage‑inducible protein/UPF0126 family inner membrane protein | |||||
| * | ? | NC_000913 | = 2729926 | NA (NA) | 3 (0.040) | 3/204 | 6.8 | NA | noncoding (1232/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 2729930 = | NA (NA) | noncoding (1228/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | = 224998 | 5 (0.070) | 3 (0.040) | 3/204 | 6.8 | 37.5% | noncoding (1228/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 225002 = | NA (NA) | noncoding (1232/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||