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 246 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,634,382 | 0 | T | C | 62.9% | ‑5.1 / 36.6 | 35 | K168K (AAA→AAG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,404 | 0 | A | G | 61.4% | ‑5.6 / 45.5 | 44 | I161T (ATC→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,388 | 0 | T | G | 61.0% | ‑5.4 / 40.7 | 41 | A166A (GCA→GCC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 339,986 | 0 | G | A | 58.8% | 21.0 / 38.5 | 34 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 1,634,370 | 0 | T | C | 57.1% | ‑0.2 / 33.9 | 28 | V172V (GTA→GTG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,597 | 0 | C | A | 57.1% | 21.3 / 232.2 | 170 | V97F (GTT→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 339,979 | 0 | G | A | 56.2% | 10.7 / 39.5 | 32 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 1,634,699 | 0 | A | C | 55.6% | 13.9 / 181.6 | 142 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,661 | 0 | C | G | 55.6% | 31.9 / 253.8 | 163 | T75T (ACG→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,578 | 0 | T | C | 55.5% | 30.5 / 221.5 | 157 | E103G (GAA→GGA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,482 | 0 | T | C | 55.5% | 17.3 / 137.4 | 101 | N135S (AAC→AGC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,484 | 0 | G | T | 55.5% | 19.6 / 147.9 | 101 | N134K (AAC→AAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,004 | 0 | C | T | 55.0% | 116.2 / inf | 281 | intergenic (‑111/+180) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,569 | 0 | A | T | 55.0% | 39.3 / 282.1 | 152 | F106Y (TTT→TAT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,134 | 0 | T | C | 54.9% | 53.4 / inf | 235 | intergenic (‑241/+50) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 580,119 | 0 | A | G | 54.8% | 63.7 / 307.8 | 211 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 1,634,724 | 0 | G | A | 54.8% | 18.1 / 169.6 | 127 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 580,115 | 0 | C | T | 54.7% | 99.0 / 298.0 | 212 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,020 | 0 | G | A | 54.6% | 117.2 / 305.3 | 228 | R47R (AGG→AGA) | ybcW | uncharacterized protein YbcW |
| * | NC_000913 | 1,634,571 | 0 | C | T | 54.6% | 32.4 / 215.0 | 152 | E105E (GAG→GAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| Marginal new junction evidence (lowest skew 10 of 19 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 566774 | 100 (1.030) | 52 (0.540) | 24/594 | 3.2 | 33.4% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 108 (1.120) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 4606166 | 86 (0.880) | 10 (0.150) | 10/420 | 4.7 | 14.7% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 56 (0.820) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 4542690 | 156 (1.600) | 15 (0.160) | 14/580 | 5.2 | 9.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 130 (1.380) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 780629 | 101 (1.040) | 8 (0.110) | 6/446 | 6.6 | 12.1% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 41 (0.570) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | 4542682 = | 151 (1.550) | 12 (0.130) | 9/580 | 6.8 | 8.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 130 (1.380) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 781222 | 50 (0.510) | 5 (0.070) | 5/446 | 7.1 | 8.8% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 66 (0.910) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 2518116 | 73 (0.750) | 4 (0.060) | 4/436 | 7.5 | 7.5% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 46 (0.650) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 4392437 | 92 (0.950) | 4 (0.060) | 4/442 | 7.6 | 5.3% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 74 (1.030) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 2521006 | 100 (1.030) | 4 (0.060) | 4/446 | 7.7 | 6.0% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521249 = | 50 (0.690) | intergenic (+1/‑4) | valY/lysV | tRNA‑Val/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 1286906 | 46 (0.470) | 6 (0.070) | 6/558 | 7.9 | 21.9% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 0 (0.000) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||