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 | 1,286,965 | 0 | A | G | 61.2% | 73.1 / 112.9 | 121 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 1,287,143 | 0 | G | A | 60.0% | 12.6 / 11.3 | 15 | noncoding (94/171 nt) P12S (CCA→TCA) | rttR tpr | rtT sRNA, processed from tyrT transcript protamine‑like protein |
| * | NC_000913 | 2,857,144 | 0 | C | T | 57.6% | ‑3.3 / 60.7 | 36 | L18F (CTC→TTC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,277 | 0 | C | T | 55.2% | 21.2 / 189.6 | 143 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,142 | 0 | A | G | 52.8% | 2.5 / 42.2 | 36 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 52.8% | ‑3.1 / 58.4 | 36 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,145 | 0 | T | A | 52.8% | ‑2.2 / 57.9 | 36 | L18H (CTC→CAC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,146 | 0 | C | G | 52.8% | ‑1.2 / 66.6 | 36 | L18L (CTC→CTG) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | T | 52.8% | 59.9 / 55.5 | 36 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | C | 52.8% | 57.1 / 59.3 | 36 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,205 | 0 | T | C | 48.0% | 2.2 / 184.6 | 127 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,245 | 0 | G | A | 47.9% | 34.1 / 178.3 | 140 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,141 | 1 | . | G | 47.2% | 53.7 / 76.9 | 36 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,173 | 0 | C | G | 44.4% | 56.0 / 213.3 | 126 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,143 | 1 | . | A | 38.9% | 4.2 / 65.5 | 36 | coding (51/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,304,914 | 0 | A | G | 37.5% | 5.7 / 12.5 | 16 | intergenic (+521/+194) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913 | 566,323 | 0 | C | T | 36.8% | 99.3 / 84.9 | 95 | pseudogene (54/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,101,857 | 0 | G | A | 36.0% | 8.4 / 14.8 | 25 | intergenic (‑113/+38) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator |
| * | NC_000913 | 566,326 | 0 | T | C | 35.8% | 74.8 / 89.8 | 95 | pseudogene (51/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 4,171,557 | 0 | C | A | 35.3% | 20.0 / 14.7 | 17 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| 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 | 35 (0.550) | 13 (0.200) | 8/202 | 4.8 | 42.6% | 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 | 3474019 = | 69 (1.080) | 3 (0.050) | 3/192 | 6.8 | 4.2% | coding (63/540 nt) | rpsG | 30S ribosomal subunit protein S7 |
| ? | NC_000913 | 3474048 = | 73 (1.200) | coding (34/540 nt) | rpsG | 30S ribosomal subunit protein S7 | |||||
| * | ? | NC_000913 | 578799 = | 56 (0.870) | 3 (0.050) | 3/198 | 6.9 | 5.3% | coding (95/294 nt) | borD | DLP12 prophage, putative lipoprotein |
| ? | NC_000913 | 578807 = | 52 (0.830) | coding (87/294 nt) | borD | DLP12 prophage, putative lipoprotein | |||||
| * | ? | NC_000913 | = 244981 | 89 (1.390) | 3 (0.050) | 3/196 | 6.9 | 3.4% | coding (655/768 nt) | yafJ | type 2 glutamine amidotransferase family protein |
| ? | NC_000913 | = 244989 | 85 (1.370) | coding (663/768 nt) | yafJ | type 2 glutamine amidotransferase family protein | |||||