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 | 1,286,965 | 0 | A | G | 62.5% | 35.7 / 77.0 | 88 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 4,171,557 | 0 | C | A | 59.3% | ‑4.2 / 37.5 | 27 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| * | NC_000913 | 566,173 | 0 | C | G | 57.9% | 70.1 / 170.4 | 107 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,205 | 0 | T | C | 55.3% | 50.2 / 119.0 | 103 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,245 | 0 | G | A | 53.9% | 7.6 / 96.0 | 76 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 1,287,143 | 0 | G | A | 52.0% | ‑3.4 / 29.3 | 25 | noncoding (94/171 nt) P12S (CCA→TCA) | rttR tpr | rtT sRNA, processed from tyrT transcript protamine‑like protein |
| * | NC_000913 | 566,277 | 0 | C | T | 50.0% | 10.4 / 104.5 | 80 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 1,287,044 | 0 | G | A | 47.1% | 10.9 / 38.3 | 34 | intergenic (+518/+22) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 1,287,048 | 0 | A | C | 40.5% | 32.1 / 54.8 | 37 | intergenic (+522/+18) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 4,518,992 | 0 | C | . | 39.3% | 184.2 / 119.4 | 84 | pseudogene (272/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 1,287,052 | 0 | A | G | 38.2% | 20.1 / 34.4 | 35 | intergenic (+526/+14) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 4,518,958 | 0 | C | A | 36.8% | 127.6 / 68.8 | 57 | pseudogene (238/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 4,518,963 | 0 | C | G | 36.7% | 124.2 / 77.7 | 60 | pseudogene (243/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 4,518,966 | 0 | A | G | 36.7% | 73.5 / 61.6 | 60 | pseudogene (246/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 566,323 | 0 | C | T | 32.2% | 120.7 / 65.6 | 87 | pseudogene (54/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,326 | 0 | T | C | 31.8% | 90.3 / 75.0 | 88 | pseudogene (51/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 1,287,024 | 0 | G | A | 28.9% | 56.8 / 26.5 | 45 | intergenic (+498/+42) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 566,332 | 0 | T | G | 27.6% | 155.0 / 92.5 | 87 | pseudogene (45/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 4,296,060 | 0 | C | T | 27.3% | 119.5 / 39.4 | 66 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,287,037 | 0 | C | T | 26.5% | 37.4 / 16.2 | 34 | intergenic (+511/+29) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| 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 | 53 (1.110) | 7 (0.170) | 7/184 | 2.9 | 14.3% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 39 (0.960) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 381788 | NA (NA) | 3 (0.060) | 3/212 | 4.7 | NA | noncoding (529/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381804 | NA (NA) | noncoding (545/1331 nt) | IS2 | repeat region | |||||