mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 27 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 38.0% | 157.8 / 81.1 | 137 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,429,984 | 0 | T | G | 34.2% | 110.7 / 37.3 | 73 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 1,825,061 | 0 | G | A | 32.1% | 91.4 / 25.1 | 56 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.5% | 143.9 / 46.6 | 89 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 650,809 | 0 | T | G | 30.8% | 121.0 / 17.1 | 65 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 888,014 | 0 | T | G | 28.2% | 157.0 / 17.9 | 85 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.1% | 233.2 / 20.8 | 130 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 501,564 | 0 | A | C | 26.7% | 141.0 / 35.2 | 75 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.0% | 140.8 / 32.2 | 73 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.8% | 118.2 / 25.1 | 62 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,240,985 | 0 | T | G | 25.7% | 149.1 / 19.6 | 75 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 445,558 | 0 | A | C | 25.4% | 102.2 / 24.2 | 55 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 501,575 | 0 | A | C | 25.4% | 131.8 / 18.7 | 67 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,101,507 | 0 | T | G | 25.3% | 205.3 / 11.7 | 95 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 29,496 | 0 | T | A | 25.0% | 139.2 / 22.1 | 60 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,906,769 | 0 | A | C | 25.0% | 121.3 / 11.0 | 60 | Y98D (TAT→GAT) | rlmA | 23S rRNA m(1)G745 methyltransferase |
| * | NC_000913 | 501,572 | 0 | A | C | 24.6% | 137.2 / 10.1 | 65 | V556G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,098,155 | 0 | A | C | 24.3% | 290.0 / 18.4 | 137 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 646,747 | 0 | T | G | 24.1% | 103.4 / 22.2 | 54 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 372,640 | 0 | T | G | 23.5% | 141.4 / 12.4 | 68 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 88 (0.760) | 21 (0.200) | 17/246 | 3.8 | 20.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 87 (0.850) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 86 (0.740) | 10 (0.090) | 10/260 | 5.9 | 9.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 114 (1.050) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 4 (0.050) | 4/192 | 6.9 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 92 (0.790) | 7 (0.060) | 7/260 | 7.0 | 6.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 115 (1.060) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1411899 = | 140 (1.200) | 3 (0.030) | 3/226 | 8.3 | 2.8% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 94 (0.990) | pseudogene (51/51 nt) | ttcC | putative tRNA 2‑thiocytidine (s(2)C32) synthase | |||||
| * | ? | NC_000913 | 1870170 = | 142 (1.220) | 4 (0.040) | 4/260 | 8.4 | 3.7% | coding (1216/1284 nt) | yeaH | DUF444 domain‑containing protein YeaH |
| ? | NC_000913 | 1870461 = | 76 (0.700) | coding (77/1476 nt) | cdgI | putative c‑di‑GMP binding protein CdgI | |||||
| * | ? | NC_000913 | 1466746 = | 100 (0.860) | 5 (0.050) | 4/262 | 8.4 | 4.9% | pseudogene (1355/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | 1466858 = | 100 (0.910) | pseudogene (1467/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | 1466452 = | 128 (1.100) | 5 (0.050) | 4/262 | 8.4 | 4.3% | pseudogene (1061/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | 1466858 = | 100 (0.910) | pseudogene (1467/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | = 2728251 | NA (NA) | 4 (0.040) | 4/268 | 8.5 | NA | noncoding (934/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | = 2728340 | NA (NA) | noncoding (845/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 4227241 | 70 (0.600) | 3 (0.030) | 3/260 | 9.0 | 4.4% | coding (3414/3684 nt) | metH | cobalamin‑dependent methionine synthase |
| ? | NC_000913 | = 4227342 | 66 (0.610) | coding (3515/3684 nt) | metH | cobalamin‑dependent methionine synthase | |||||