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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 47.0% | 45.2 / 56.8 | 67 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 39.5% | 40.4 / 23.8 | 38 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 372,640 | 0 | T | G | 35.2% | 69.6 / 25.5 | 54 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 29,496 | 0 | T | A | 31.2% | 85.6 / 24.3 | 48 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 28.6% | 137.4 / 14.8 | 70 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 753,125 | 0 | T | A | 28.1% | 116.9 / 22.0 | 57 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 26.7% | 82.8 / 15.9 | 45 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,775,467 | 0 | A | C | 26.3% | 106.3 / 14.0 | 57 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 3,240,985 | 0 | T | G | 24.5% | 108.7 / 14.0 | 53 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 4,032,731 | 0 | T | G | 24.3% | 143.0 / 17.7 | 70 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 501,564 | 0 | A | C | 23.5% | 67.1 / 10.7 | 34 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.4% | 157.7 / 34.2 | 77 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 646,747 | 0 | T | G | 23.3% | 82.5 / 18.6 | 43 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 753,114 | 0 | G | T | 22.9% | 165.3 / 11.4 | 61 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,512,048 | 0 | A | C | 22.9% | 154.0 / 11.1 | 70 | L123V (TTG→GTG) | fecD | ferric citrate ABC transporter membrane subunit FecD |
| * | NC_000913 | 1,489,174 | 0 | G | T | 22.2% | 166.8 / 15.4 | 63 | G315C (GGT→TGT) | aldA | aldehyde dehydrogenase A |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.3% | 161.2 / 13.5 | 76 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 1,577,123 | 0 | A | C | 20.5% | 156.9 / 12.0 | 73 | V166G (GTA→GGA) | yddB | putative TonB‑dependent receptor |
| * | NC_000913 | 3,206,435 | 0 | C | T | 20.0% | 112.7 / 14.0 | 50 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 43 (0.480) | 12 (0.140) | 12/258 | 4.7 | 19.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 58 (0.690) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 46 (0.510) | 12 (0.140) | 11/258 | 5.0 | 19.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 58 (0.690) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 64 (0.710) | 13 (0.160) | 10/244 | 5.0 | 16.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 73 (0.920) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1207790 = | 68 (0.760) | 10 (0.130) | 10/244 | 5.0 | 12.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 76 (0.960) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 4 (0.060) | 4/190 | 6.3 | 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 | = 2423194 | 117 (1.310) | 5 (0.060) | 5/258 | 7.3 | 4.5% | coding (346/891 nt) | rpnB | recombination‑promoting nuclease RpnB |
| ? | NC_000913 | = 2423287 | 104 (1.240) | coding (253/891 nt) | rpnB | recombination‑promoting nuclease RpnB | |||||
| * | ? | NC_000913 | = 2518182 | 88 (0.980) | 3 (0.040) | 3/248 | 8.2 | 3.9% | noncoding (50/76 nt) | alaW | tRNA‑Ala |
| ? | NC_000913 | = 2521099 | 67 (0.830) | noncoding (49/76 nt) | valX | tRNA‑Val | |||||
| * | ? | NC_000913 | = 1209618 | 91 (1.020) | 4 (0.050) | 3/246 | 8.2 | 5.3% | pseudogene (38/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment |
| ? | NC_000913 | 2471897 = | 61 (0.760) | pseudogene (166/519 nt) | yfdL | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 3 (0.040) | 3/258 | 8.4 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 3638374 = | 72 (0.800) | 3 (0.040) | 3/260 | 8.5 | 3.7% | coding (733/1500 nt) | pitA | metal phosphate:H(+) symporter PitA |
| ? | NC_000913 | 3638535 = | 89 (1.050) | coding (894/1500 nt) | pitA | metal phosphate:H(+) symporter PitA | |||||