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 24 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 | 60.9% | 28.7 / 63.8 | 69 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 2,857,144 | 0 | C | T | 60.0% | 2.8 / 49.3 | 32 | L18F (CTC→TTC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,145 | 0 | T | A | 59.4% | 11.5 / 42.9 | 32 | L18H (CTC→CAC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,146 | 0 | C | G | 59.4% | 16.7 / 48.6 | 32 | L18L (CTC→CTG) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | T | 59.4% | 56.0 / 42.4 | 32 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | C | 58.1% | 53.4 / 44.6 | 32 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,142 | 0 | A | G | 56.2% | 5.3 / 33.2 | 32 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 56.2% | 2.4 / 47.1 | 32 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 4,171,557 | 0 | C | A | 55.6% | ‑0.7 / 47.0 | 27 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,296,060 | 0 | C | T | 49.2% | 17.2 / 84.1 | 65 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 2,857,141 | 1 | . | G | 43.8% | ‑5.3 / 63.5 | 32 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,277 | 0 | C | T | 40.0% | 75.4 / 91.2 | 90 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,245 | 0 | G | A | 39.7% | 61.2 / 71.5 | 73 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,173 | 0 | C | G | 39.4% | 71.7 / 102.2 | 71 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,143 | 1 | . | A | 37.5% | 10.5 / 55.9 | 32 | coding (51/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,323 | 0 | C | T | 36.7% | 79.8 / 70.8 | 80 | pseudogene (54/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,205 | 0 | T | C | 34.4% | 50.4 / 57.6 | 61 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,326 | 0 | T | C | 32.5% | 84.3 / 69.3 | 83 | pseudogene (51/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,332 | 0 | T | G | 31.7% | 120.4 / 96.2 | 82 | pseudogene (45/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 3,728,110 | 2 | . | C | 29.2% | 32.9 / 25.9 | 24 | coding (1262/1455 nt) | xylB | xylulokinase |
| 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 | 32 (0.680) | 7 (0.180) | 6/178 | 3.0 | 18.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 36 (0.910) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1323147 | 52 (1.110) | 13 (0.280) | 5/210 | 3.7 | 33.3% | 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 | 2765212 = | 76 (1.620) | 3 (0.070) | 3/194 | 4.3 | 4.1% | intergenic (‑59/+301) | yfjL/yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage, uncharacterized protein |
| ? | NC_000913 | 2765237 = | 70 (1.610) | intergenic (‑84/+276) | yfjL/yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage, uncharacterized protein | |||||
| * | ? | NC_000913 | = 2066538 | 4 (0.090) | 3 (0.070) | 3/198 | 4.4 | 44.3% | noncoding (816/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2102132 | NA (NA) | noncoding (812/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 274334 | NA (NA) | 3 (0.070) | 3/198 | 4.4 | NA | noncoding (816/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 274338 | NA (NA) | noncoding (812/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1598612 | 50 (1.060) | 5 (0.110) | 3/210 | 4.5 | 9.2% | intergenic (‑625/+5) | yneO/lsrK | pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase |
| ? | NC_000913 | 1598618 = | 49 (1.040) | coding (1592/1593 nt) | lsrK | autoinducer‑2 (AI‑2) kinase | |||||