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 258 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 339,979 | 0 | G | A | 64.6% | 45.7 / 42.5 | 50 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,986 | 0 | G | A | 64.0% | 47.9 / 46.6 | 50 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 580,120 | 0 | C | T | 62.4% | 309.8 / inf | 306 | intergenic (+34/+131) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,115 | 0 | C | T | 62.4% | 333.1 / inf | 303 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,119 | 0 | A | G | 62.1% | 276.6 / inf | 306 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 1,634,676 | 0 | A | G | 58.3% | 19.1 / 295.6 | 223 | D70D (GAT→GAC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 580,020 | 0 | G | A | 58.1% | 222.3 / inf | 322 | R47R (AGG→AGA) | ybcW | uncharacterized protein YbcW |
| * | NC_000913 | 1,634,724 | 0 | G | A | 58.1% | 6.6 / 235.5 | 191 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 578,605 | 0 | T | G | 57.8% | 179.7 / inf | 277 | K97Q (AAA→CAA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,427 | 0 | G | C | 57.6% | 86.4 / 296.7 | 198 | T107T (ACG→ACC) R34P (CGG→CCG) | rzpD rzoD | putative prophage endopeptidase RzpD putative prophage lysis lipoprotein RzoD |
| * | NC_000913 | 1,634,404 | 0 | A | G | 57.4% | 0.2 / 73.4 | 61 | I161T (ATC→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,414 | 0 | C | T | 57.4% | ‑0.9 / 78.2 | 68 | E158K (GAG→AAG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,661 | 0 | C | G | 57.3% | 38.6 / inf | 234 | T75T (ACG→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,699 | 0 | A | C | 56.9% | 20.4 / 279.6 | 209 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 578,571 | 0 | C | T | 56.6% | 134.9 / inf | 274 | intergenic (+3/+29) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 578,574 | 0 | A | C | 56.5% | 176.7 / inf | 276 | intergenic (+6/+26) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 579,099 | 0 | A | . | 56.5% | 66.9 / inf | 315 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,831 | 0 | T | C | 56.2% | 129.3 / inf | 309 | T21T (ACA→ACG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 1,634,658 | 0 | A | G | 56.1% | 43.9 / inf | 239 | V76V (GTT→GTC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 578,811 | 0 | T | G | 56.0% | 165.4 / inf | 275 | Q28P (CAG→CCG) | borD | prophage lipoprotein BorD |
| Marginal new junction evidence (lowest skew 10 of 30 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2819229 | 41 (0.390) | 33 (0.310) | 25/598 | 3.2 | 44.6% | intergenic (‑83/+152) | csrA/alaS | carbon storage regulator/alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| ? | NC_000913 | = 3187426 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 3128997 | 71 (0.670) | 28 (0.260) | 24/598 | 3.4 | 28.3% | coding (726/765 nt) | glcC | DNA‑binding transcriptional dual regulator GlcC |
| ? | NC_000913 | 3130146 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 566774 | 116 (1.090) | 57 (0.540) | 20/594 | 4.1 | 32.8% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 118 (1.120) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 1313978 = | 107 (1.010) | 19 (0.180) | 18/598 | 4.5 | 15.1% | intergenic (‑315/‑42) | yciC/ompW | putative inner membrane protein/outer membrane protein W |
| ? | NC_000913 | = 1651548 | NA (NA) | noncoding (706/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 4542682 = | 165 (1.550) | 18 (0.170) | 17/580 | 4.6 | 10.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 152 (1.470) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 2819225 = | 46 (0.430) | 22 (0.210) | 17/596 | 4.7 | 32.4% | intergenic (‑79/+156) | csrA/alaS | carbon storage regulator/alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| ? | NC_000913 | = 2997691 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 4542690 | 178 (1.680) | 20 (0.190) | 16/580 | 4.8 | 11.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 152 (1.470) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 16 (0.150) | 16/598 | 4.9 | 11.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 658887 = | 119 (1.120) | intergenic (‑949/‑60) | crcB/tatE | F(‑) channel protein/twin arginine protein translocation system ‑ TatE protein | |||||
| * | ? | NC_000913 | = 696741 | 76 (0.720) | 10 (0.130) | 9/442 | 5.4 | 15.7% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 51 (0.650) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 2521006 | 73 (0.690) | 8 (0.100) | 8/446 | 5.8 | 14.5% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521249 = | 40 (0.500) | intergenic (+1/‑4) | valY/lysV | tRNA‑Val/tRNA‑Lys | |||||