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 29 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 | 63.8% | 103.1 / 57.6 | 47 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | . | 63.8% | 24.8 / 79.4 | 47 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | . | 63.8% | 37.0 / 73.3 | 47 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,144 | 0 | C | G | 63.0% | 71.2 / 55.5 | 47 | L18V (CTC→GTC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 1 | . | A | 61.7% | 95.1 / 58.1 | 47 | coding (51/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,173 | 0 | C | G | 56.4% | 60.4 / 198.8 | 117 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 1,286,965 | 0 | A | G | 56.0% | 14.0 / 92.0 | 84 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 3,742,599 | 0 | C | . | 55.6% | ‑1.6 / 128.5 | 63 | intergenic (‑67/‑134) | yiaJ/yiaK | transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent |
| * | NC_000913 | 566,205 | 0 | T | C | 53.4% | 37.9 / 123.2 | 103 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,245 | 0 | G | A | 50.0% | 8.2 / 109.1 | 84 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,277 | 0 | C | T | 48.4% | 19.5 / 116.9 | 94 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 4,171,557 | 0 | C | A | 45.5% | 26.5 / 49.8 | 33 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| * | NC_000913 | 3,742,598 | 0 | C | . | 44.4% | 119.8 / 102.0 | 63 | intergenic (‑66/‑135) | yiaJ/yiaK | transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent |
| * | NC_000913 | 2,857,142 | 0 | A | G | 36.2% | 35.5 / 41.1 | 47 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 36.2% | 53.7 / 51.8 | 47 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,145 | 0 | T | A | 36.2% | 55.2 / 51.0 | 47 | L18H (CTC→CAC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,146 | 0 | C | G | 36.2% | 63.4 / 57.7 | 47 | L18L (CTC→CTG) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 34.6% | 104.6 / 61.6 | 79 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 4,518,992 | 0 | C | . | 34.4% | 284.7 / 149.7 | 122 | pseudogene (272/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 1,287,143 | 0 | G | A | 28.0% | 23.3 / 11.5 | 25 | noncoding (94/171 nt) P12S (CCA→TCA) | rttR tpr | rtT sRNA, processed from tyrT transcript protamine‑like 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 | 1286708 = | 41 (0.560) | 20 (0.340) | 11/166 | 3.1 | 46.7% | intergenic (+182/+358) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| ? | NC_000913 | = 1287241 | 13 (0.220) | intergenic (‑5/+3) | rttR/tyrV | rtT sRNA, processed from tyrT transcript/tRNA‑Tyr | |||||
| * | ? | NC_000913 | 4542682 = | 35 (0.480) | 6 (0.090) | 6/190 | 5.1 | 9.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 80 (1.200) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 2786739 | 82 (1.130) | 9 (0.130) +ATT |
6/202 | 5.4 | 10.2% | pseudogene (343/2253 nt) | ygaQ | uncharacterized protein, putative enzyme |
| ? | NC_000913 | = 2786745 | 82 (1.130) | pseudogene (349/2253 nt) | ygaQ | uncharacterized protein, putative enzyme | |||||
| * | ? | NC_000913 | = 4542690 | 38 (0.520) | 4 (0.060) | 4/190 | 6.0 | 6.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 80 (1.200) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||