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 193 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,386,862 | 0 | G | A | 63.2% | 12.8 / 34.7 | 38 | intergenic (+31/‑72) | yfbL/yfbM | putative M28A family peptidase/DUF1877 family protein |
| * | NC_000913 | 283,931 | 0 | T | G | 60.9% | 7.5 / 17.2 | 25 | V244G (GTG→GGG) | yagF | CP4‑6 prophage; dehydratase family protein |
| * | NC_000913 | 357,890 | 0 | C | A | 60.9% | ‑6.5 / 21.4 | 23 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 1,246,518 | 0 | T | G | 57.9% | 8.6 / 21.2 | 19 | T287P (ACC→CCC) | treA | periplasmic trehalase |
| * | NC_000913 | 354,288 | 0 | T | G | 56.8% | 23.0 / 49.8 | 37 | V528G (GTG→GGG) | prpE | propionate‑‑CoA ligase |
| * | NC_000913 | 328,791 | 0 | A | G | 56.2% | 3.3 / 16.1 | 17 | S182P (TCC→CCC) | betI | choline‑inducible betIBA‑betT divergent operon transcriptional repressor |
| * | NC_000913 | 2,378,968 | 0 | C | T | 55.9% | 2.8 / 30.0 | 34 | E98K (GAA→AAA) | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| * | NC_000913 | 2,008,351 | 0 | T | G | 54.5% | 29.9 / 45.7 | 33 | G25G (GGT→GGG) | yedE | UPF0394 family sulphur transport domain‑containing inner membrane protein |
| * | NC_000913 | 3,575,956 | 0 | A | C | 53.3% | 1.2 / 13.0 | 17 | V369G (GTG→GGG) | gntU | gluconate transporter, low affinity GNT 1 system |
| * | NC_000913 | 3,665,698 | 0 | T | C | 53.1% | 28.1 / 72.8 | 51 | D38G (GAT→GGT) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 1,356,201 | 0 | T | G | 52.9% | 5.3 / 19.3 | 17 | T304P (ACC→CCC) | sapA | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,760,384 | 0 | A | C | 52.8% | 7.0 / 30.4 | 36 | V289G (GTG→GGG) | selA | selenocysteine synthase |
| * | NC_000913 | 1,383,722 | 0 | G | A | 52.0% | 6.7 / 31.4 | 25 | F80F (TTC→TTT) | ycjW | LacI family putative transcriptional repressor |
| * | NC_000913 | 657,676 | 0 | A | C | 51.8% | 16.5 / 35.4 | 27 | V88G (GTG→GGG) | flc | fluoride efflux channel, dual topology membrane protein |
| * | NC_000913 | 2,889,472 | 0 | T | G | 51.8% | 21.4 / 31.5 | 27 | T210P (ACC→CCC) | cysI | sulfite reductase, beta subunit, NAD(P)‑binding, heme‑binding |
| * | NC_000913 | 3,556,207 | 0 | T | C | 51.8% | 16.3 / 36.0 | 27 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 29,496 | 0 | T | A | 50.0% | 25.5 / 30.0 | 36 | intergenic (+301/‑155) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| * | NC_000913 | 650,458 | 0 | A | G | 50.0% | 39.1 / 12.5 | 40 | T11T (ACT→ACC) | citE | citrate lyase, citryl‑ACP lyase (beta) subunit |
| * | NC_000913 | 4,604,344 | 0 | C | T | 50.0% | 25.0 / 33.2 | 50 | S62F (TCT→TTT) | bglJ | bgl operon transcriptional activator |
| * | NC_000913 | 650,464 | 0 | A | T | 48.7% | 22.8 / 25.1 | 40 | R9R (CGT→CGA) | citE | citrate lyase, citryl‑ACP lyase (beta) subunit |
| Marginal new junction evidence (lowest skew 10 of 31 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2713829 | 39 (0.950) | 8 (0.210) | 6/276 | 3.2 | 17.4% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase |
| ? | NC_000913 | = 2713908 | 40 (1.050) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | = 3592583 | 31 (0.840) | 5 (0.130) | 5/270 | 3.5 | 13.9% | noncoding (20/99 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 | = 3592647 | NA (NA) | noncoding (84/99 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 | = 398392 | 45 (1.100) | 4 (0.110) | 4/270 | 3.9 | 8.7% | coding (521/1095 nt) | yaiW | microcin Bac7 uptake protein; outer membrane surface‑exposed lipoprotein |
| ? | NC_000913 | = 398378 | 43 (1.160) | coding (507/1095 nt) | yaiW | microcin Bac7 uptake protein; outer membrane surface‑exposed lipoprotein | |||||
| * | ? | NC_000913 | = 3403865 | 31 (0.760) | 4 (0.110) | 4/276 | 4.0 | 11.2% | coding (382/975 nt) | acuI | putative acryloyl‑CoA reductase |
| ? | NC_000913 | = 3403959 | 35 (0.920) | coding (476/975 nt) | acuI | putative acryloyl‑CoA reductase | |||||
| * | ? | NC_000913 | 2852106 = | 48 (1.170) | 4 (0.100) | 4/282 | 4.1 | 8.7% | coding (243/273 nt) | hypC | hydrogenase maturation protein |
| ? | NC_000913 | 2852166 = | 39 (1.010) | coding (31/1122 nt) | hypD | hydrogenase maturation protein | |||||
| * | ? | NC_000913 | = 1827132 | 37 (0.900) | 4 (0.100) | 4/280 | 4.1 | 9.9% | coding (1128/1344 nt) | astB | succinylarginine dihydrolase |
| ? | NC_000913 | = 1827166 | 38 (0.990) | coding (1094/1344 nt) | astB | succinylarginine dihydrolase | |||||
| * | ? | NC_000913 | 1136017 = | 37 (0.900) | 4 (0.100) | 4/280 | 4.1 | 10.4% | coding (454/699 nt) | flgH | flagellar protein of basal‑body outer‑membrane L ring |
| ? | NC_000913 | 1136038 = | 34 (0.880) | coding (475/699 nt) | flgH | flagellar protein of basal‑body outer‑membrane L ring | |||||
| * | ? | NC_000913 | = 2518231 | 46 (1.120) | 3 (0.090) +23 bp |
3/252 | 4.2 | 7.2% | noncoding (1/76 nt) | alaW | tRNA‑Ala |
| ? | NC_000913 | = 3427077 | NA (NA) | noncoding (76/77 nt) | ileU | tRNA‑Ile | |||||
| * | ? | NC_000913 | = 2518117 | 31 (0.760) | 3 (0.090) +22 bp |
3/254 | 4.2 | 10.2% | intergenic (‑1/+39) | alaX/alaW | tRNA‑Ala/tRNA‑Ala |
| ? | NC_000913 | = 3427077 | NA (NA) | noncoding (76/77 nt) | ileU | tRNA‑Ile | |||||
| * | ? | NC_000913 | 225456 = | 4 (0.100) | 3 (0.090) +23 bp |
3/252 | 4.2 | 12.4% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 2518231 | 46 (1.120) | noncoding (1/76 nt) | alaW | tRNA‑Ala | |||||