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 30 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,171,557 | 0 | C | A | 67.9% | 6.4 / 33.7 | 28 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| * | NC_000913 | 2,857,141 | 1 | . | G | 67.7% | 70.1 / 30.7 | 31 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | . | 67.7% | 25.9 / 42.9 | 31 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | . | 67.7% | 32.8 / 40.5 | 31 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,144 | 0 | C | G | 63.0% | 42.2 / 29.3 | 31 | L18V (CTC→GTC) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,277 | 0 | C | T | 61.7% | 72.6 / 122.3 | 115 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,205 | 0 | T | C | 59.9% | 138.7 / 170.2 | 167 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,173 | 0 | C | G | 57.9% | 120.6 / 287.6 | 178 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 1,286,965 | 0 | A | G | 57.9% | 40.0 / 168.7 | 159 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 2,857,143 | 1 | . | A | 54.8% | 54.3 / 44.8 | 31 | coding (51/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,245 | 0 | G | A | 54.1% | 10.9 / 181.4 | 135 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 3,738,736 | 0 | G | A | 49.7% | 30.9 / 201.2 | 157 | A414T (GCT→ACT) | malS | alpha‑amylase |
| * | NC_000913 | 566,323 | 0 | C | T | 40.9% | 73.4 / 115.5 | 110 | pseudogene (54/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,326 | 0 | T | C | 40.5% | 43.7 / 128.2 | 111 | pseudogene (51/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 3,728,110 | 1 | . | C | 40.2% | 38.4 / 187.5 | 102 | coding (1262/1455 nt) | xylB | xylulokinase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 40.0% | 81.9 / 91.2 | 90 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 3,713,539 | 0 | A | . | 37.4% | 312.9 / 185.7 | 147 | coding (448/564 nt) | tag | 3‑methyl‑adenine DNA glycosylase I, constitutive |
| * | NC_000913 | 566,332 | 0 | T | G | 36.9% | 91.4 / 168.0 | 111 | pseudogene (45/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,142 | 0 | A | G | 32.3% | 27.6 / 23.4 | 31 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 32.3% | 46.2 / 24.9 | 31 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair 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 | 1207790 = | 92 (1.120) | 14 (0.200) | 13/174 | 3.3 | 16.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 62 (0.890) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 81 (0.980) | 9 (0.130) | 9/174 | 4.4 | 12.1% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 62 (0.890) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 4542682 = | 21 (0.260) | 6 (0.080) | 6/188 | 5.8 | 12.9% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 62 (0.830) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 20 (0.240) | 4 (0.050) | 4/188 | 6.7 | 9.1% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 62 (0.830) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 2092986 = | 334 (4.060) | 3 (0.040) | 3/178 | 7.1 | 0.99% | coding (589/1071 nt) | hisC | histidinol‑phosphate aminotransferase |
| ? | NC_000913 | = 2092981 | 309 (4.350) | coding (584/1071 nt) | hisC | histidinol‑phosphate aminotransferase | |||||
| * | ? | NC_000913 | 2733439 = | 89 (1.080) | 4 (0.050) | 3/192 | 7.4 | 5.6% | coding (735/2574 nt) | clpB | protein disaggregation chaperone |
| ? | NC_000913 | 3301761 = | 52 (0.680) | coding (277/996 nt) | yhbU | U32 peptidase family protein | |||||
| * | ? | NC_000913 | = 2668554 | 71 (0.860) | 3 (0.040) | 3/198 | 7.5 | 4.2% | coding (343/891 nt) | hcaR | hca operon transcriptional regulator |
| ? | NC_000913 | = 2668555 | 68 (0.860) | coding (342/891 nt) | hcaR | hca operon transcriptional regulator | |||||
| * | ? | NC_000913 | = 2762944 | 100 (1.220) | 3 (0.040) | 3/202 | 7.6 | 3.0% | coding (597/2190 nt) | yfjK | radiation resistance protein, DEAD/H helicase‑like protein, CP4‑57 putative defective prophage |
| ? | NC_000913 | 2762951 = | 97 (1.200) | coding (590/2190 nt) | yfjK | radiation resistance protein, DEAD/H helicase‑like protein, CP4‑57 putative defective prophage | |||||
| * | ? | NC_000913 | = 2225875 | 98 (1.190) | 3 (0.040) | 3/202 | 7.6 | 3.2% | coding (75/579 nt) | yohD | DedA family inner membrane protein |
| ? | NC_000913 | = 2225908 | 84 (1.040) | coding (108/579 nt) | yohD | DedA family inner membrane protein | |||||