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 | 38.2% | 147.0 / 70.5 | 110 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 34.0% | 71.4 / 32.6 | 50 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,556,207 | 0 | T | C | 34.0% | 72.9 / 21.7 | 50 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.0% | 87.0 / 21.8 | 50 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,205 | 0 | A | C | 31.2% | 88.2 / 17.3 | 48 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 28.6% | 167.6 / 40.0 | 91 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 753,125 | 0 | T | A | 28.1% | 61.2 / 10.9 | 32 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 26.9% | 165.7 / 28.6 | 78 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.2% | 119.9 / 33.7 | 61 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.1% | 127.4 / 19.6 | 46 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 175,694 | 0 | T | G | 25.8% | 122.7 / 14.0 | 62 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 3,206,444 | 0 | T | A | 25.0% | 101.8 / 11.7 | 48 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,404,218 | 0 | T | G | 24.7% | 191.1 / 31.7 | 89 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.7% | 167.2 / 47.9 | 81 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 646,747 | 0 | T | G | 23.4% | 100.7 / 20.5 | 47 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 23.4% | 150.3 / 20.5 | 77 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,032,731 | 0 | T | G | 23.3% | 133.3 / 16.6 | 60 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 445,558 | 0 | A | C | 22.4% | 110.6 / 18.3 | 49 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,135,775 | 0 | C | T | 21.7% | 157.2 / 15.1 | 69 | K199K (AAG→AAA) | pitB | metal phosphate:H(+) symporter PitB |
| * | NC_000913 | 1,068,173 | 0 | T | G | 20.7% | 201.7 / 20.0 | 82 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 77 (0.800) | 7 (0.080) | 7/256 | 6.0 | 9.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 65 (0.730) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 58075 | 0 (0.000) | 4 (0.050) +CGGTTAAAGGG |
4/252 | 7.2 | 74.4% | coding (712/816 nt) | djlA | co‑chaperone protein DjlA |
| ? | NC_000913 | 60688 = | 3 (0.030) | coding (2577/2907 nt) | rapA | RNA polymerase‑binding ATPase and RNAP recycling factor | |||||
| * | ? | NC_000913 | = 3653112 | NA (NA) | 3 (0.030) | 3/270 | 8.1 | 20.2% | noncoding (119/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3653116 = | 12 (0.130) | noncoding (115/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3366632 | NA (NA) | 3 (0.030) | 3/270 | 8.1 | 25.3% | noncoding (119/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3366636 = | 9 (0.090) | noncoding (115/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3130260 | NA (NA) | 3 (0.030) | 3/270 | 8.1 | NA | noncoding (115/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3130264 = | NA (NA) | noncoding (119/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2289995 | NA (NA) | 3 (0.030) | 3/270 | 8.1 | 15.2% | noncoding (119/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2289999 = | 17 (0.180) | noncoding (115/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2102825 | NA (NA) | 3 (0.030) | 3/270 | 8.1 | 27.6% | noncoding (119/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2102829 = | 8 (0.080) | noncoding (115/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1603002 = | 108 (1.130) | 3 (0.030) | 3/272 | 8.1 | 3.0% | coding (1513/1536 nt) | lsrA | Autoinducer‑2 ABC transporter ATP binding subunit |
| ? | NC_000913 | = 1603162 | 88 (0.930) | coding (144/1029 nt) | lsrC | Autoinducer‑2 ABC transporter membrane subunit LsrC | |||||
| * | ? | NC_000913 | = 1396158 | 15 (0.160) | 3 (0.030) | 3/270 | 8.1 | 16.9% | noncoding (115/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1396162 = | NA (NA) | noncoding (119/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1299613 | NA (NA) | 3 (0.030) | 3/270 | 8.1 | NA | noncoding (115/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1299617 = | NA (NA) | noncoding (119/1195 nt) | IS5 | repeat region | |||||