mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 151 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,228,236 | 0 | G | C | 44.4% | 29.8 / 10.5 | 27 | pseudogene (374/1287 nt) | mdtQ | pseudogene; putative channel/filament proteins |
| * | NC_000913 | 3,745,019 | 0 | C | G | 43.8% | 17.3 / 26.8 | 48 | G72G (GGC→GGG) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 433,649 | 0 | T | G | 39.7% | 41.4 / 24.2 | 71 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 3,206,446 | 0 | C | A | 36.1% | 77.7 / 21.2 | 62 | intergenic (‑190/‑17) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 3,026,941 | 0 | A | C | 36.0% | 98.1 / 11.5 | 50 | E392D (GAA→GAC) | guaD | guanine deaminase |
| * | NC_000913 | 811,721 | 0 | T | G | 34.2% | 136.8 / 15.3 | 77 | V67G (GTG→GGG) | bioC | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 1,445,981 | 0 | T | G | 33.3% | 125.6 / 13.5 | 60 | G34G (GGT→GGG) | ydbL | DUF1318 family protein |
| * | NC_000913 | 3,005,991 | 0 | G | A | 33.3% | 60.4 / 12.7 | 42 | intergenic (‑205/‑271) | ygeV/ygeW | putative sigma‑54‑interacting transcriptional activator/putative carbamoyltransferase |
| * | NC_000913 | 3,731,713 | 0 | G | A | 33.3% | 102.2 / 20.4 | 63 | E195K (GAA→AAA) | xylF | D‑xylose transporter subunit |
| * | NC_000913 | 4,101,514 | 0 | G | T | 33.3% | 110.4 / 18.9 | 54 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter |
| * | NC_000913 | 1,239,823 | 0 | T | G | 32.7% | 116.8 / 10.8 | 56 | G315G (GGT→GGG) | dadX | alanine racemase, catabolic, PLP‑binding |
| * | NC_000913 | 75,023 | 0 | A | C | 32.1% | 84.0 / 10.1 | 54 | V153G (GTG→GGG) | thiB | thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,846,683 | 0 | G | T | 31.8% | 127.7 / 16.1 | 66 | Q244K (CAA→AAA) | hycD | hydrogenase 3, membrane subunit |
| * | NC_000913 | 2,151,689 | 0 | G | T | 31.6% | 51.3 / 14.2 | 57 | intergenic (+43/+22) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 433,634 | 0 | T | G | 31.2% | 111.4 / 17.3 | 80 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 1,159,837 | 0 | A | G | 31.0% | 110.5 / 14.3 | 58 | I572T (ATC→ACC) | fhuE | ferric‑rhodotorulic acid outer membrane transporter |
| * | NC_000913 | 540,558 | 0 | T | G | 30.9% | 176.2 / 26.0 | 84 | intergenic (+50/‑7) | allB/ybbY | allantoinase/putative uracil/xanthine transporter |
| * | NC_000913 | 1,258,996 | 0 | T | G | 30.8% | 131.0 / 20.0 | 78 | V69G (GTG→GGG) | ychH | DUF2583 family putative inner membrane protein |
| * | NC_000913 | 1,478,324 | 0 | T | G | 30.8% | 130.1 / 11.2 | 52 | G33G (GGT→GGG) | ynbB | putative CDP‑diglyceride synthase |
| * | NC_000913 | 3,665,702 | 0 | C | A | 30.6% | 194.0 / 24.3 | 85 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| Marginal new junction evidence (lowest skew 10 of 412 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 86 (0.840) | 25 (0.270) | 22/324 | 3.4 | 24.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 78 (0.830) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 80 (0.780) | 18 (0.190) | 16/324 | 4.6 | 19.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 77 (0.820) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 18 (0.190) | 16/330 | 4.7 | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 2170358 | 11 (0.110) | 18 (0.190) | 13/330 | 5.5 | 63.8% | noncoding (188/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 2170558 | NA (NA) | noncoding (388/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 1819454 | 92 (0.890) | 19 (0.190) | 14/346 | 5.5 | 15.5% | intergenic (‑7/+1) | chbR/chbA | repressor of chb operon for N,N'‑diacetylchitobiose utilization/N,N'‑diacetylchitobiose‑specific enzyme IIA component of PTS |
| ? | NC_000913 | = 1819721 | 118 (1.180) | coding (85/351 nt) | chbA | N,N'‑diacetylchitobiose‑specific enzyme IIA component of PTS | |||||
| * | ? | NC_000913 | 1095115 = | NA (NA) | 18 (0.190) | 13/330 | 5.5 | 61.8% | noncoding (388/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 1095315 = | 12 (0.120) | noncoding (188/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 566964 | 20 (0.190) | 18 (0.190) | 13/330 | 5.5 | 49.3% | noncoding (188/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 567164 | NA (NA) | noncoding (388/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 392579 = | NA (NA) | 18 (0.190) | 13/330 | 5.5 | 56.4% | noncoding (388/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 392779 = | 15 (0.150) | noncoding (188/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315413 | 12 (0.120) | 18 (0.190) | 13/330 | 5.5 | 61.8% | noncoding (185/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315613 | NA (NA) | noncoding (385/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 2730267 | NA (NA) | 30 (0.300) | 13/344 | 5.7 | NA | noncoding (891/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 2730343 | NA (NA) | noncoding (815/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon | |||||