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 226 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 | 59.4% | ‑5.4 / 174.6 | 143 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,661 | 0 | C | G | 58.9% | 2.4 / 258.1 | 175 | T75T (ACG→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,676 | 0 | A | G | 58.3% | 0.6 / 206.0 | 168 | D70D (GAT→GAC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,699 | 0 | A | C | 58.3% | 1.1 / 196.5 | 156 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,658 | 0 | A | G | 57.8% | 7.1 / 222.3 | 180 | V76V (GTT→GTC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,271 | 0 | G | A | 56.8% | 120.4 / inf | 288 | H108H (CAC→CAT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,597 | 0 | C | A | 56.3% | 26.3 / 255.3 | 174 | V97F (GTT→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,385 | 0 | A | G | 56.3% | 167.8 / inf | 334 | N70N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,457 | 0 | A | G | 56.1% | 157.0 / inf | 327 | I46I (ATT→ATC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,285 | 0 | T | C | 56.0% | 123.5 / inf | 285 | I104V (ATT→GTT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,484 | 0 | G | T | 55.9% | 17.3 / 150.7 | 102 | N134K (AAC→AAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,717 | 0 | A | C | 55.6% | 199.3 / inf | 358 | intergenic (‑123/‑163) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,540 | 0 | T | C | 55.5% | 179.6 / inf | 374 | N19D (AAC→GAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,502 | 0 | A | G | 55.1% | 141.4 / inf | 379 | N31N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,578 | 0 | T | C | 55.1% | 32.2 / 226.3 | 166 | E103G (GAA→GGA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,569 | 0 | A | T | 54.9% | 38.7 / 313.8 | 163 | F106Y (TTT→TAT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,571 | 0 | C | T | 54.9% | 33.5 / 236.6 | 162 | E105E (GAG→GAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,482 | 0 | T | C | 54.9% | 14.8 / 133.9 | 102 | N135S (AAC→AGC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,651 | 0 | C | T | 54.9% | 104.9 / inf | 350 | intergenic (‑57/‑229) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 1,634,404 | 0 | A | G | 54.8% | 5.4 / 51.6 | 42 | I161T (ATC→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 566774 | 112 (1.100) | 58 (0.580) | 25/594 | 3.2 | 33.8% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 116 (1.150) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 3648146 | 122 (1.200) | 18 (0.220) | 14/482 | 4.4 | 15.4% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 99 (1.210) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 1287329 | 65 (0.640) | 9 (0.130) | 8/424 | 5.7 | 18.0% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 36 (0.500) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 696741 | 75 (0.740) | 10 (0.130) | 8/442 | 5.9 | 15.2% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 56 (0.750) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 781222 | 52 (0.510) | 7 (0.090) | 7/446 | 6.4 | 13.6% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 50 (0.660) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 696616 | 79 (0.780) | 4 (0.060) +117 bp |
4/364 | 6.7 | 8.2% | noncoding (1/75 nt) | glnV | tRNA‑Gln |
| ? | NC_000913 | 696664 = | 69 (0.680) | noncoding (77/77 nt) | metU | tRNA‑Met | |||||
| * | ? | NC_000913 | = 4606166 | 113 (1.110) | 5 (0.070) | 5/420 | 7.0 | 6.2% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 73 (1.020) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2357730 | 125 (1.230) | 7 (0.080) | 7/518 | 7.2 | 6.1% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 108 (1.230) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 780629 | 89 (0.880) | 5 (0.070) | 5/446 | 7.3 | 7.9% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 50 (0.660) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | 4542682 = | 153 (1.510) | 10 (0.100) | 8/580 | 7.4 | 7.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 119 (1.210) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||