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 266 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 | 68.9% | 8.3 / 37.3 | 45 | K168K (AAA→AAG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,388 | 0 | T | G | 65.3% | 1.2 / 47.0 | 49 | A166A (GCA→GCC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,404 | 0 | A | G | 63.6% | ‑1.4 / 49.7 | 55 | I161T (ATC→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,370 | 0 | T | C | 60.0% | ‑4.4 / 50.3 | 45 | V172V (GTA→GTG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,482 | 0 | T | C | 53.2% | 33.7 / 169.0 | 124 | N135S (AAC→AGC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,484 | 0 | G | T | 52.4% | 41.6 / 193.4 | 124 | N134K (AAC→AAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,271 | 0 | G | A | 52.2% | 23.3 / inf | 295 | H108H (CAC→CAT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,385 | 0 | A | G | 52.1% | 46.9 / inf | 335 | N70N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,285 | 0 | T | C | 51.8% | 25.5 / inf | 304 | I104V (ATT→GTT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,457 | 0 | A | G | 51.7% | 35.8 / inf | 346 | I46I (ATT→ATC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,571 | 0 | C | T | 51.3% | 13.4 / inf | 230 | intergenic (+3/+29) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 578,605 | 0 | T | G | 51.1% | 50.7 / inf | 235 | K97Q (AAA→CAA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 1,634,578 | 0 | T | C | 51.0% | 81.1 / 290.4 | 194 | E103G (GAA→GGA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 578,574 | 0 | A | C | 50.9% | 60.1 / inf | 233 | intergenic (+6/+26) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 579,146 | 0 | A | G | 50.8% | 6.2 / inf | 254 | intergenic (‑253/+38) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,569 | 0 | A | T | 50.0% | 91.6 / inf | 191 | F106Y (TTT→TAT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 578,729 | 0 | A | G | 49.8% | 0.8 / inf | 268 | A55A (GCT→GCC) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 1,634,571 | 0 | C | T | 49.7% | 82.3 / 306.0 | 191 | E105E (GAG→GAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,724 | 0 | G | A | 49.7% | 62.0 / 241.1 | 158 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,134 | 0 | T | C | 49.6% | 4.6 / inf | 244 | intergenic (‑241/+50) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 166 (1.490) | 18 (0.170) | 16/580 | 5.2 | 10.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 139 (1.280) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 566774 | 93 (0.830) | 54 (0.490) | 15/594 | 5.6 | 33.9% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 118 (1.060) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 4542682 = | 150 (1.340) | 13 (0.120) | 12/580 | 6.3 | 8.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 139 (1.280) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2653419 | 94 (0.840) | 9 (0.090) | 9/548 | 7.1 | 9.0% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 96 (0.940) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 781222 | 72 (0.650) | 6 (0.070) | 5/446 | 7.7 | 9.3% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 63 (0.760) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4094350 | 76 (0.680) | 6 (0.060) | 6/516 | 8.0 | 9.0% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094719 = | 56 (0.580) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 2521006 | 86 (0.770) | 6 (0.070) | 4/446 | 8.2 | 9.4% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521249 = | 52 (0.620) | intergenic (+1/‑4) | valY/lysV | tRNA‑Val/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 780918 | 71 (0.640) | 4 (0.050) | 4/446 | 8.2 | 7.3% | noncoding (76/76 nt) | lysW | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 49 (0.590) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 1286906 | 69 (0.620) | 8 (0.080) | 6/558 | 8.5 | 10.7% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 69 (0.660) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 3469040 | 101 (0.910) | 6 (0.060) | 5/558 | 9.0 | 5.2% | coding (814/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469344 = | 126 (1.210) | coding (510/2694 nt) | chiA | endochitinase | |||||