mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 91 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,173,361 | 0 | C | . | 76.9% | 71.9 / 15.9 | 26 | pseudogene (2/442 nt) | gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| * | NC_000913 | 281,089 | 0 | A | C | 71.4% | ‑1.5 / 12.3 | 21 | Y299D (TAT→GAT) | yagA | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 2,151,689 | 0 | G | T | 64.7% | 12.8 / 6.5 | 35 | intergenic (+43/+22) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 2,228,222 | 0 | T | G | 62.5% | 0.1 / 11.6 | 16 | pseudogene (388/1287 nt) | mdtQ | pseudogene; putative channel/filament proteins |
| * | NC_000913 | 2,386,862 | 0 | G | A | 62.5% | 0.0 / 13.2 | 17 | intergenic (+31/‑72) | yfbL/yfbM | putative M28A family peptidase/DUF1877 family protein |
| * | NC_000913 | 4,223,620 | 0 | T | G | 61.1% | 1.3 / 11.5 | 18 | A3A (GCA→GCC) | iclR | transcriptional repressor |
| * | NC_000913 | 3,575,947 | 0 | A | C | 60.0% | 6.9 / 13.5 | 15 | V372G (GTT→GGT) | gntU | gluconate transporter, low affinity GNT 1 system |
| * | NC_000913 | 3,813,072 | 0 | A | C | 58.8% | 5.0 / 14.7 | 17 | T114T (ACA→ACC) | dfp | fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding |
| * | NC_000913 | 2,337,723 | 0 | A | C | 58.3% | 3.6 / 11.3 | 13 | G566G (GGT→GGG) | gyrA | DNA gyrase (type II topoisomerase), subunit A |
| * | NC_000913 | 4,223,597 | 0 | C | T | 57.9% | ‑3.5 / 10.7 | 19 | R11K (AGA→AAA) | iclR | transcriptional repressor |
| * | NC_000913 | 4,223,634 | 0 | T | G | 56.2% | 10.7 / 19.2 | 16 | intergenic (‑6/‑194) | iclR/metH | transcriptional repressor/homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| * | NC_000913 | 4,111,747 | 0 | G | T | 56.0% | 10.9 / 36.1 | 25 | N156K (AAC→AAA) | yiiQ | DUF1454 family putative periplasmic protein |
| * | NC_000913 | 1,072,731 | 0 | T | G | 55.6% | 13.9 / 20.7 | 18 | T45P (ACC→CCC) | rutB | ureidoacrylate amidohydrolase |
| * | NC_000913 | 4,223,614 | 0 | A | G | 55.6% | 8.4 / 21.7 | 18 | I5I (ATT→ATC) | iclR | transcriptional repressor |
| * | NC_000913 | 345,328 | 0 | C | A | 55.0% | 23.0 / 66.4 | 40 | intergenic (+337/‑76) | yahL/yahM | uncharacterized protein/uncharacterized protein |
| * | NC_000913 | 354,318 | 0 | T | G | 55.0% | 10.1 / 25.9 | 20 | V538G (GTG→GGG) | prpE | propionate‑‑CoA ligase |
| * | NC_000913 | 2,480,371 | 0 | T | G | 55.0% | 15.8 / 26.1 | 20 | G390G (GGT→GGG) | dsdA | D‑serine dehydratase |
| * | NC_000913 | 993,913 | 0 | G | C | 54.5% | 1.7 / 15.1 | 12 | G44G (GGC→GGG) | ssuB | aliphatic sulfonate ABC transporter ATPase |
| * | NC_000913 | 1,755,871 | 0 | T | A | 54.5% | 0.6 / 27.5 | 23 | G58G (GGT→GGA) | pykF | pyruvate kinase I |
| * | NC_000913 | 1,973,535 | 0 | T | C | 54.5% | 4.7 / 12.7 | 11 | D597G (GAT→GGT) | cheA | fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing 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 = | 21 (0.800) | 3 (0.130) | 3/266 | 2.7 | 14.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 17 (0.730) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3497094 = | 29 (1.110) | 3 (0.120) | 3/274 | 2.8 | 9.7% | coding (92/807 nt) | nirC | nitrite transporter |
| ? | NC_000913 | 3497106 = | 29 (1.200) | coding (104/807 nt) | nirC | nitrite transporter | |||||
| * | ? | NC_000913 | 1647054 = | 22 (0.840) | 3 (0.120) | 3/276 | 2.8 | 14.2% | intergenic (+317/+120) | flxA/intK | Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related |
| ? | NC_000913 | 1647120 = | 16 (0.660) | intergenic (+383/+54) | flxA/intK | Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 4481898 | 15 (0.570) | 3 (0.120) | 3/282 | 2.9 | 17.5% | coding (1940/2856 nt) | valS | valyl‑tRNA synthetase |
| ? | NC_000913 | = 4481970 | 14 (0.560) | coding (1868/2856 nt) | valS | valyl‑tRNA synthetase | |||||
| * | ? | NC_000913 | 3566202 = | 31 (1.180) | 3 (0.120) | 3/282 | 2.9 | 9.0% | coding (380/2448 nt) | glgP | glycogen phosphorylase |
| ? | NC_000913 | 3566229 = | 31 (1.250) | coding (353/2448 nt) | glgP | glycogen phosphorylase | |||||
| * | ? | NC_000913 | = 3340296 | 30 (1.140) | 3 (0.120) | 3/280 | 2.9 | 9.3% | coding (22/978 nt) | yrbG | putative calcium/sodium:proton antiporter |
| ? | NC_000913 | = 3340323 | 30 (1.220) | coding (49/978 nt) | yrbG | putative calcium/sodium:proton antiporter | |||||