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 1337 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,386,862 | 0 | G | A | 60.8% | 33.7 / 104.2 | 97 | intergenic (+31/‑72) | yfbL/yfbM | putative M28A family peptidase/DUF1877 family protein |
| * | NC_000913 | 3,665,698 | 0 | T | C | 57.3% | 33.9 / 178.8 | 144 | D38G (GAT→GGT) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 3,665,702 | 0 | C | A | 56.9% | 55.0 / 190.4 | 144 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 3,686,028 | 0 | T | C | 54.9% | 75.6 / 127.2 | 93 | E1049G (GAG→GGG) | bcsC | cellulose synthase subunit |
| * | NC_000913 | 354,288 | 0 | T | G | 53.8% | 91.5 / 124.4 | 78 | V528G (GTG→GGG) | prpE | propionate‑‑CoA ligase |
| * | NC_000913 | 357,890 | 0 | C | A | 53.6% | ‑0.5 / 58.1 | 56 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 3,813,272 | 0 | C | T | 51.2% | 35.0 / 97.7 | 82 | S181L (TCG→TTG) | dfp | fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding |
| * | NC_000913 | 357,880 | 0 | T | C | 50.8% | 55.3 / 103.2 | 65 | K271E (AAA→GAA) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 2,332,823 | 0 | A | G | 50.8% | 119.3 / 192.4 | 132 | pseudogene (1580/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| * | NC_000913 | 3,640,981 | 0 | C | T | 49.5% | 47.0 / 72.6 | 100 | F40F (TTC→TTT) | dtpB | dipeptide and tripeptide permease B |
| * | NC_000913 | 1,356,201 | 0 | T | G | 48.6% | 99.2 / 20.2 | 73 | T304P (ACC→CCC) | sapA | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,133,302 | 0 | T | G | 48.4% | 105.5 / 47.0 | 97 | H219P (CAC→CCC) | yghS | putative ATP‑binding protein |
| * | NC_000913 | 657,676 | 0 | A | C | 48.2% | 147.8 / 40.4 | 115 | V88G (GTG→GGG) | flc | fluoride efflux channel, dual topology membrane protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 48.1% | 53.8 / 82.6 | 104 | intergenic (‑179/‑28) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 1,222,233 | 0 | G | A | 46.0% | 54.1 / 43.6 | 75 | pseudogene (60/75 nt) | ycgH | pseudogene; putative ATP‑binding component of a transport system |
| * | NC_000913 | 2,571,036 | 0 | T | G | 45.7% | 93.6 / 15.0 | 71 | N239T (AAC→ACC) | eutE | aldehyde oxidoreductase, ethanolamine utilization protein |
| * | NC_000913 | 540,558 | 0 | T | G | 45.6% | 104.5 / 44.3 | 92 | intergenic (+50/‑7) | allB/ybbY | allantoinase/putative uracil/xanthine transporter |
| * | NC_000913 | 364,526 | 0 | C | A | 45.5% | 111.3 / 53.8 | 100 | G594C (GGC→TGC) | lacZ | beta‑D‑galactosidase |
| * | NC_000913 | 3,443,277 | 0 | A | C | 45.1% | 126.0 / 50.5 | 91 | V274G (GTA→GGA) | secY | preprotein translocase membrane subunit |
| * | NC_000913 | 3,686,021 | 0 | A | C | 45.1% | 135.9 / 15.0 | 91 | G1051G (GGT→GGG) | bcsC | cellulose synthase subunit |
| Marginal new junction evidence (lowest skew 10 of 194 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 381689 | NA (NA) | 21 (0.200) | 13/278 | 6.1 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 12 (0.120) | 9/278 | 7.7 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2756112 | 112 (1.020) | 9 (0.090) | 8/274 | 8.0 | 7.7% | intergenic (+734/‑47) | smpB/intA | tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase |
| ? | NC_000913 | = 2756129 | 111 (1.090) | intergenic (+751/‑30) | smpB/intA | tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase | |||||
| * | ? | NC_000913 | 3381839 = | 89 (0.810) | 9 (0.090) | 8/278 | 8.1 | 9.4% | coding (1097/1368 nt) | degQ | serine endoprotease, periplasmic |
| ? | NC_000913 | 3381869 = | 89 (0.860) | coding (1127/1368 nt) | degQ | serine endoprotease, periplasmic | |||||
| * | ? | NC_000913 | = 2547356 | 119 (1.080) | 11 (0.110) | 8/278 | 8.1 | 9.0% | coding (684/1425 nt) | murP | N‑acetylmuramic acid permease, EIIBC component, PTS system |
| ? | NC_000913 | = 2547371 | 112 (1.090) | coding (699/1425 nt) | murP | N‑acetylmuramic acid permease, EIIBC component, PTS system | |||||
| * | ? | NC_000913 | 3060398 = | 88 (0.800) | 9 (0.090) | 8/280 | 8.2 | 9.9% | coding (646/894 nt) | argP | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| ? | NC_000913 | 3060457 = | 80 (0.770) | coding (705/894 nt) | argP | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor | |||||
| * | ? | NC_000913 | = 2169291 | 115 (1.050) | 8 (0.080) | 8/280 | 8.2 | 6.6% | coding (580/900 nt) | yegS | phosphatidylglycerol kinase, metal‑dependent |
| ? | NC_000913 | = 2169311 | 118 (1.140) | coding (600/900 nt) | yegS | phosphatidylglycerol kinase, metal‑dependent | |||||
| * | ? | NC_000913 | 2765420 = | 122 (1.110) | 5 (0.060) | 4/208 | 8.3 | 6.3% | intergenic (‑267/+93) | yfjL/yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein |
| ? | NC_000913 | = 2765411 | 64 (0.830) | intergenic (‑258/+102) | yfjL/yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | 3592584 = | NA (NA) | 7 (0.070) | 7/268 | 8.4 | 7.3% | noncoding (21/99 nt) | RIP258 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP258 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3592648 = | 89 (0.900) | noncoding (85/99 nt) | RIP258 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP258 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 3927418 = | 105 (0.960) | 8 (0.080) | 7/272 | 8.5 | 7.6% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 98 (0.970) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||