mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 31 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,728,110 | 2 | . | C | 70.4% | 61.7 / 23.0 | 27 | coding (1262/1455 nt) | xylB | xylulokinase |
| * | NC_000913 | 1,286,965 | 0 | A | G | 55.7% | 22.1 / 107.4 | 97 | intergenic (+439/+101) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| * | NC_000913 | 2,857,141 | 1 | . | G | 55.6% | 67.8 / 53.6 | 36 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | . | 55.6% | 48.5 / 74.5 | 36 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | . | 55.6% | ‑3.9 / 69.9 | 36 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,173 | 0 | C | G | 53.0% | 28.2 / 212.1 | 115 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,205 | 0 | T | C | 51.0% | 22.5 / 129.2 | 100 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 2,857,144 | 0 | C | G | 50.0% | 15.4 / 50.0 | 36 | L18V (CTC→GTC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 375,067 | 0 | A | G | 47.4% | ‑1.7 / 23.6 | 19 | intergenic (+186/‑392) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| * | NC_000913 | 4,171,557 | 0 | C | A | 47.4% | 8.8 / 26.3 | 19 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| * | NC_000913 | 375,075 | 0 | G | A | 46.7% | ‑1.4 / 13.9 | 15 | intergenic (+194/‑384) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| * | NC_000913 | 1,287,143 | 0 | G | A | 44.4% | ‑5.4 / 15.5 | 18 | noncoding (94/171 nt) P12S (CCA→TCA) | rttR tpr | rtT sRNA, processed from tyrT transcript protamine‑like protein |
| * | NC_000913 | 2,857,142 | 0 | A | G | 44.4% | 6.4 / 39.0 | 36 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 44.4% | 17.5 / 46.5 | 36 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 1 | . | A | 44.4% | 50.8 / 76.2 | 36 | coding (51/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,145 | 0 | T | A | 44.4% | 16.9 / 47.8 | 36 | L18H (CTC→CAC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,146 | 0 | C | G | 44.4% | 21.2 / 54.1 | 36 | L18L (CTC→CTG) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 357,857 | 0 | G | A | 42.7% | 53.2 / 85.7 | 82 | A278A (GCC→GCT) | cynR | transcriptional activator of cyn operon, autorepressor |
| * | NC_000913 | 566,277 | 0 | C | T | 37.2% | 84.7 / 79.5 | 86 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,245 | 0 | G | A | 37.1% | 66.2 / 62.4 | 70 | pseudogene (132/279 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 | = 1207805 | 30 (0.520) | 8 (0.170) | 8/170 | 3.6 | 17.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 52 (1.070) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 3855959 | 47 (0.820) | 16 (0.280) | 7/200 | 4.5 | 22.6% | coding (12/363 nt) | yidG | inner membrane protein |
| ? | NC_000913 | = 3855988 | 63 (1.100) | coding (320/348 nt) | yidH | DUF202 family inner membrane protein | |||||
| * | ? | NC_000913 | = 1323147 | 43 (0.750) | 15 (0.260) | 7/202 | 4.5 | 40.5% | 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 | = 40600 | 58 (1.010) | 3 (0.050) | 3/196 | 6.2 | 5.1% | coding (1332/1515 nt) | caiT | putative transporter |
| ? | NC_000913 | 40604 = | 56 (1.000) | coding (1328/1515 nt) | caiT | putative transporter | |||||