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 21 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,101,857 | 0 | G | A | 64.0% | 8.7 / 21.3 | 25 | intergenic (‑113/+38) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator |
| * | NC_000913 | 2,857,144 | 0 | C | T | 52.0% | 14.5 / 106.7 | 53 | L18F (CTC→TTC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 1,286,965 | 0 | A | G | 51.0% | ‑1.0 / 186.8 | 147 | 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 | 50.9% | 91.8 / 92.2 | 53 | coding (49/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,147 | 0 | A | . | 50.9% | 81.8 / 125.0 | 53 | coding (55/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,148 | 0 | G | . | 50.9% | 79.5 / 116.9 | 53 | coding (56/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,142 | 0 | A | G | 49.1% | ‑4.3 / 72.4 | 53 | Y17C (TAT→TGT) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,143 | 0 | T | A | 49.1% | 10.6 / 79.6 | 53 | Y17* (TAT→TAA) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,145 | 0 | T | A | 49.1% | 12.2 / 78.1 | 53 | L18H (CTC→CAC) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 2,857,146 | 0 | C | G | 49.1% | 18.1 / 87.0 | 53 | L18L (CTC→CTG) ‡ | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 566,245 | 0 | G | A | 48.5% | 27.7 / 123.6 | 101 | pseudogene (132/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,277 | 0 | C | T | 48.2% | 34.7 / 138.2 | 112 | pseudogene (100/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,173 | 0 | C | G | 47.7% | 15.5 / 248.7 | 130 | pseudogene (204/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,205 | 0 | T | C | 47.3% | ‑1.9 / 159.4 | 110 | pseudogene (172/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 4,171,557 | 0 | C | A | 46.3% | 26.7 / 66.6 | 41 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| * | NC_000913 | 2,857,143 | 1 | . | A | 45.3% | 79.4 / 116.8 | 53 | coding (51/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| * | NC_000913 | 1,287,143 | 0 | G | A | 40.0% | 0.1 / 21.2 | 25 | noncoding (94/171 nt) P12S (CCA→TCA) | rttR tpr | rtT sRNA, processed from tyrT transcript protamine‑like protein |
| * | NC_000913 | 566,323 | 0 | C | T | 29.4% | 190.0 / 81.3 | 119 | pseudogene (54/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,326 | 0 | T | C | 28.0% | 166.2 / 92.7 | 125 | pseudogene (51/279 nt) | exoD | pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related |
| * | NC_000913 | 566,332 | 0 | T | G | 27.6% | 231.9 / 134.7 | 127 | pseudogene (45/279 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 | 66 (0.860) | 35 (0.460) | 15/216 | 3.4 | 51.1% | intergenic (‑65/‑73) | trpL/yciV | trp operon leader peptide/PHP domain protein |
| ? | NC_000913 | = 3742633 | 1 (0.010) | intergenic (‑101/‑100) | yiaJ/yiaK | transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent | |||||
| * | ? | NC_000913 | = 380012 | 49 (0.710) | 13 (0.170) +GGG |
9/190 | 4.4 | 20.4% | intergenic (‑131/+57) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| ? | NC_000913 | 380013 = | 50 (0.650) | intergenic (‑132/+56) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein | |||||
| * | ? | NC_000913 | 105361 = | 30 (0.390) | 4 (0.060) | 4/192 | 6.5 | 13.0% | coding (57/1152 nt) | ftsZ | GTP‑binding tubulin‑like cell division protein |
| ? | NC_000913 | = 105357 | 27 (0.400) | coding (53/1152 nt) | ftsZ | GTP‑binding tubulin‑like cell division protein | |||||
| * | ? | NC_000913 | = 4542690 | 22 (0.290) | 4 (0.060) | 4/198 | 6.6 | 8.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 63 (0.900) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 1821202 | 42 (0.550) | 4 (0.060) +GGATGCAAG |
3/198 | 7.1 | 9.0% | coding (13/1359 nt) | chbC | N,N'‑diacetylchitobiose‑specific enzyme IIC component of PTS |
| ? | NC_000913 | = 2148961 | 46 (0.600) | coding (1288/1353 nt) | yegD | Hsp70 chaperone family protein | |||||
| * | ? | NC_000913 | = 1543150 | 57 (0.750) | 3 (0.040) | 3/208 | 7.4 | 5.2% | coding (911/1389 nt) | narU | nitrate/nitrite transporter |
| ? | NC_000913 | 1543155 = | 54 (0.730) | coding (906/1389 nt) | narU | nitrate/nitrite transporter | |||||
| * | ? | NC_000913 | = 983622 | 79 (1.030) | 4 (0.050) | 3/210 | 7.4 | 4.9% | coding (548/549 nt) | ycbK | M15A protease‑related family periplasmic protein |
| ? | NC_000913 | 983626 = | 79 (1.060) | intergenic (+3/‑24) | ycbK/ycbL | M15A protease‑related family periplasmic protein/putative metal‑binding enzyme | |||||
| * | ? | NC_000913 | = 604399 | 84 (1.100) | 3 (0.040) | 3/210 | 7.4 | 3.4% | coding (265/1248 nt) | ybdG | mechanosensitive channel protein, miniconductance |
| ? | NC_000913 | 604404 = | 87 (1.170) | coding (260/1248 nt) | ybdG | mechanosensitive channel protein, miniconductance | |||||