mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 251 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,634,724 | 0 | G | A | 60.3% | ‑3.4 / 165.0 | 141 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,699 | 0 | A | C | 60.2% | 3.9 / 180.0 | 162 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,661 | 0 | C | G | 59.7% | ‑1.5 / 252.4 | 176 | T75T (ACG→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,676 | 0 | A | G | 59.4% | ‑2.2 / 219.8 | 170 | D70D (GAT→GAC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,569 | 0 | A | T | 58.1% | 5.9 / 272.5 | 155 | F106Y (TTT→TAT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,571 | 0 | C | T | 58.1% | 0.3 / 206.6 | 155 | E105E (GAG→GAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,597 | 0 | C | A | 58.0% | 7.8 / 230.2 | 169 | V97F (GTT→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,578 | 0 | T | C | 57.7% | 2.7 / 202.6 | 158 | E103G (GAA→GGA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,658 | 0 | A | G | 56.6% | 18.6 / 246.5 | 183 | V76V (GTT→GTC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 580,115 | 0 | C | T | 55.1% | 82.8 / 255.0 | 185 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 1,634,482 | 0 | T | C | 54.0% | 15.0 / 139.6 | 100 | N135S (AAC→AGC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,484 | 0 | G | T | 54.0% | 15.9 / 149.1 | 100 | N134K (AAC→AAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 580,119 | 0 | A | G | 53.8% | 30.6 / 276.9 | 184 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 579,285 | 0 | T | C | 53.7% | 47.5 / inf | 246 | I104V (ATT→GTT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 580,120 | 0 | C | T | 53.5% | 59.0 / 267.7 | 185 | intergenic (+34/+131) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 578,571 | 0 | C | T | 53.1% | 64.0 / inf | 241 | intergenic (+3/+29) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 578,605 | 0 | T | G | 52.7% | 55.0 / inf | 241 | K97Q (AAA→CAA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,574 | 0 | A | C | 52.7% | 90.1 / inf | 243 | intergenic (+6/+26) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 579,717 | 0 | A | C | 52.6% | 117.2 / inf | 323 | intergenic (‑123/‑163) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,271 | 0 | G | A | 52.5% | 44.3 / inf | 240 | H108H (CAC→CAT) | ybcV | DUF1398 domain‑containing protein YbcV |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 382179 = | NA (NA) | 29 (0.280) | 22/594 | 3.6 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 4542690 | 165 (1.600) | 25 (0.250) | 21/580 | 3.7 | 15.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 117 (1.170) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 152 (1.470) | 25 (0.250) | 20/580 | 3.9 | 15.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 117 (1.170) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 566774 | 102 (0.990) | 39 (0.380) | 18/594 | 4.4 | 28.5% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 94 (0.920) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 4606166 | 121 (1.170) | 8 (0.110) | 8/420 | 5.5 | 9.4% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 70 (0.970) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 3648146 | 147 (1.420) | 8 (0.100) | 8/482 | 6.2 | 6.8% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 100 (1.200) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 9 (0.090) | 7/598 | 7.8 | 9.0% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 543175 | 91 (0.880) | intergenic (+142/+86) | glxK/allE | glycerate 2‑kinase 2/(S)‑ureidoglycine aminohydrolase | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 7 (0.070) | 7/598 | 7.8 | 7.2% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 543168 = | 90 (0.870) | intergenic (+135/+93) | glxK/allE | glycerate 2‑kinase 2/(S)‑ureidoglycine aminohydrolase | |||||
| * | ? | NC_000913 | = 1962523 | 97 (0.940) | 8 (0.080) | 6/596 | 8.2 | 7.6% | intergenic (+63/+57) | yecT/flhE | protein YecT/flagellar protein FlhE |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 1096961 = | 83 (0.800) | 3 (0.040) | 3/438 | 8.2 | 4.3% | intergenic (+132/+604) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 73 (0.970) | intergenic (+674/+62) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||