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 | 2,857,141 | 1 | . | G | 62.5% | 49.1 / 26.9 | 24 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | . | 58.3% | ‑3.8 / 45.0 | 24 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | . | 58.3% | 2.3 / 41.6 | 24 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,245 | 0 | G | A | 57.7% | 19.9 / 93.2 | 79 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,144 | 0 | C | G | 57.1% | 20.9 / 24.5 | 24 | L18V (CTC→GTC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,277 | 0 | C | T | 53.4% | ‑2.6 / 120.6 | 88 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 1,286,965 | 0 | A | G | 53.1% | ‑3.0 / 57.8 | 49 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 566,205 | 0 | T | C | 50.7% | 5.8 / 93.0 | 73 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,143 | 1 | . | A | 50.0% | 35.6 / 39.0 | 24 | coding (51/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,173 | 0 | C | G | 46.8% | 14.1 / 141.2 | 79 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,145 | 0 | T | A | 41.7% | 15.9 / 26.2 | 24 | L18H (CTC→CAC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,146 | 0 | C | G | 41.7% | 18.9 / 29.3 | 24 | L18L (CTC→CTG) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 1,287,044 | 0 | G | A | 41.4% | 23.4 / 27.0 | 29 | 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 | 38.7% | 34.6 / 44.4 | 31 | intergenic (+522/+18) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 2,857,142 | 0 | A | G | 37.5% | 14.6 / 17.7 | 24 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 37.5% | 28.3 / 18.4 | 24 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 4,171,557 | 0 | C | A | 35.5% | 41.1 / 33.0 | 31 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,518,992 | 0 | C | . | 35.2% | 210.1 / 112.9 | 91 | pseudogene (272/504 nt) | insB1 | IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| * | NC_000913 | 4,296,060 | 0 | C | T | 35.1% | 87.7 / 64.7 | 77 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 566,326 | 0 | T | C | 32.0% | 72.3 / 67.1 | 80 | pseudogene (51/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| 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 | 45 (0.840) | 22 (0.410) | 9/208 | 3.2 | 48.9% | intergenic (‑65/‑73) | trpL/yciV | trp operon leader peptide/PHP domain protein |
| ? | NC_000913 | = 3742633 | 1 (0.020) | intergenic (‑101/‑100) | yiaJ/yiaK | transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent | |||||
| * | ? | NC_000913 | = 4542690 | 24 (0.450) | 4 (0.080) | 4/190 | 4.5 | 12.7% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 33 (0.670) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 2820730 | 53 (0.990) | 3 (0.060) | 3/204 | 5.2 | 5.4% | coding (1282/2631 nt) | alaS | alanyl‑tRNA synthetase |
| ? | NC_000913 | 2820734 = | 53 (1.010) | coding (1278/2631 nt) | alaS | alanyl‑tRNA synthetase | |||||
| * | ? | NC_000913 | = 2441741 | 35 (0.650) | 4 (0.080) | 3/204 | 5.2 | 10.3% | intergenic (‑136/‑23) | fabB/mnmC | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase I/fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme |
| ? | NC_000913 | 2441745 = | 35 (0.670) | intergenic (‑140/‑19) | fabB/mnmC | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase I/fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme | |||||
| * | ? | NC_000913 | 2075186 = | 147 (2.740) | 3 (0.060) | 3/208 | 5.2 | 1.9% | coding (408/1533 nt) | yeeR | CP4‑44 prophage, putative membrane protein |
| ? | NC_000913 | 2075204 = | 158 (2.950) | coding (426/1533 nt) | yeeR | CP4‑44 prophage, putative membrane protein | |||||