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 | 566,173 | 0 | C | G | 62.1% | 136.6 / 194.7 | 133 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,144 | 0 | C | T | 58.3% | 0.4 / 63.9 | 38 | L18F (CTC→TTC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,205 | 0 | T | C | 57.9% | 81.3 / 129.1 | 121 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 4,171,557 | 0 | C | A | 57.5% | 0.0 / 58.9 | 40 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| * | NC_000913 | 1,286,965 | 0 | A | G | 57.1% | 13.4 / 113.8 | 105 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 2,857,142 | 0 | A | G | 55.3% | 9.7 / 41.4 | 38 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 55.3% | 1.7 / 57.4 | 38 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,145 | 0 | T | A | 55.3% | 1.8 / 57.6 | 38 | L18H (CTC→CAC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,146 | 0 | C | G | 55.3% | 1.0 / 66.6 | 38 | L18L (CTC→CTG) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | T | 55.3% | 67.0 / 55.2 | 38 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | C | 55.3% | 66.9 / 58.5 | 38 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,245 | 0 | G | A | 54.0% | 1.6 / 136.1 | 100 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,277 | 0 | C | T | 50.4% | 11.1 / 167.3 | 111 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,141 | 1 | . | G | 44.7% | 54.2 / 75.4 | 38 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 1 | . | A | 39.5% | 2.7 / 71.0 | 38 | coding (51/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 36.7% | 95.4 / 70.7 | 79 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 4,518,992 | 0 | C | . | 35.5% | 207.3 / 114.1 | 94 | pseudogene (272/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 4,518,966 | 0 | A | G | 31.2% | 124.6 / 64.6 | 77 | pseudogene (246/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 4,518,963 | 0 | C | G | 30.8% | 194.9 / 89.0 | 78 | pseudogene (243/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 4,518,958 | 0 | C | A | 30.0% | 202.6 / 79.9 | 80 | pseudogene (238/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon 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 | = 1323147 | 70 (1.010) | 21 (0.300) | 11/218 | 4.0 | 37.5% | intergenic (‑65/‑73) | trpL/yciV | trp operon leader peptide/PHP domain protein |
| ? | NC_000913 | = 3742633 | 0 (0.000) | intergenic (‑101/‑100) | yiaJ/yiaK | transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent | |||||
| * | ? | NC_000913 | 4542682 = | 23 (0.330) | 5 (0.080) | 5/200 | 5.6 | 9.6% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 73 (1.150) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 1050326 = | 7 (0.100) | 6 (0.090) | 5/216 | 6.0 | 11.7% | noncoding (549/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4519016 | 84 (1.220) | noncoding (545/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 3136999 = | 68 (0.980) | 3 (0.050) | 3/198 | 6.6 | 4.3% | coding (1524/1860 nt) | gss | glutathionylspermidine amidase and glutathionylspermidine synthetase |
| ? | NC_000913 | 3231686 = | 72 (1.140) | coding (22/2019 nt) | fadH | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked | |||||