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 262 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,208,132 | 0 | G | A | 74.3% | 211.0 / 114.1 | 172 | intergenic (‑600/‑15) | purH/rrsE | bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA |
| * | NC_000913 | 1,634,382 | 0 | T | C | 64.1% | 3.3 / 34.4 | 39 | K168K (AAA→AAG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,404 | 0 | A | G | 61.9% | 2.3 / 36.3 | 42 | I161T (ATC→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,388 | 0 | T | G | 61.5% | ‑1.3 / 34.2 | 39 | A166A (GCA→GCC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,482 | 0 | T | C | 57.8% | 7.1 / 137.1 | 116 | N135S (AAC→AGC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,484 | 0 | G | T | 57.8% | 12.4 / 160.8 | 116 | N134K (AAC→AAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,569 | 0 | A | T | 55.7% | 32.9 / inf | 203 | F106Y (TTT→TAT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,571 | 0 | C | T | 54.9% | 34.1 / 286.7 | 207 | E105E (GAG→GAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,699 | 0 | A | C | 54.7% | 22.3 / 284.8 | 213 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,724 | 0 | G | A | 54.7% | 24.6 / 248.8 | 193 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,578 | 0 | T | C | 54.6% | 35.5 / 280.3 | 210 | E103G (GAA→GGA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,597 | 0 | C | A | 54.6% | 41.8 / inf | 227 | V97F (GTT→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,661 | 0 | C | G | 54.6% | 46.6 / inf | 229 | T75T (ACG→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,370 | 0 | T | C | 54.5% | ‑2.1 / 40.2 | 33 | V172V (GTA→GTG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,676 | 0 | A | G | 54.4% | 40.1 / 298.5 | 218 | D70D (GAT→GAC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,658 | 0 | A | G | 53.2% | 51.3 / inf | 236 | V76V (GTT→GTC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,671 | 0 | T | C | 52.6% | 20.2 / inf | 342 | intergenic (‑77/‑209) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,540 | 0 | T | C | 52.1% | 55.6 / inf | 357 | N19D (AAC→GAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,427 | 0 | G | C | 51.5% | ‑4.8 / inf | 205 | T107T (ACG→ACC) R34P (CGG→CCG) | rzpD rzoD | putative prophage endopeptidase RzpD putative prophage lysis lipoprotein RzoD |
| * | NC_000913 | 579,717 | 0 | A | C | 51.4% | 64.4 / inf | 363 | intergenic (‑123/‑163) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| Marginal new junction evidence (lowest skew 10 of 36 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 166 (1.460) | 28 (0.250) | 24/570 | 2.9 | 16.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 133 (1.210) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 566774 | 133 (1.170) | 71 (0.630) | 24/584 | 3.0 | 34.5% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 138 (1.220) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 4606166 | 106 (0.930) | 12 (0.150) | 11/410 | 4.1 | 12.9% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 88 (1.110) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 781222 | 79 (0.690) | 10 (0.120) | 9/436 | 5.0 | 17.2% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 38 (0.450) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 2818275 | 75 (0.660) | 9 (0.110) | 8/430 | 5.3 | 12.7% | intergenic (‑1/+198) | argY/argV | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818551 = | 69 (0.830) | intergenic (‑2/+2) | argV/serV | tRNA‑Arg/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 1287241 | 61 (0.540) | 13 (0.130) +36 bp |
10/516 | 5.4 | 19.4% | intergenic (‑5/+3) | rttR/tyrV | small RNA RttR/tRNA‑Tyr |
| ? | NC_000913 | 1287572 = | 62 (0.550) | noncoding (51/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 696741 | 74 (0.650) | 8 (0.100) | 7/432 | 5.7 | 11.7% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 67 (0.800) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 2357652 | 141 (1.240) | 9 (0.090) | 9/520 | 5.8 | 7.7% | coding (749/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357836 = | 90 (0.890) | intergenic (+33/+206) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 2653419 | 92 (0.810) | 9 (0.090) | 9/538 | 6.0 | 8.3% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 115 (1.110) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 3469049 | 133 (1.170) | 10 (0.090) | 9/572 | 6.3 | 6.5% | coding (805/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469353 = | 157 (1.420) | coding (501/2694 nt) | chiA | endochitinase | |||||