mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 22 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,479,583 | 0 | C | T | 67.1% | 597.6 / inf | 395 | intergenic (‑46/‑147) | yjgM/yjgN | putative acetyltransferase YjgM/conserved inner membrane protein YjgN |
| * | NC_000913 | 2,046,941 | 0 | A | G | 61.9% | 275.4 / inf | 289 | E668E (GAA→GAG) | yeeJ | inverse autotransporter adhesin |
| * | NC_000913 | 3,256,179 | 0 | T | C | 61.4% | 231.1 / inf | 246 | H158R (CAC→CGC) | cyuA | putative L‑cysteine desulfidase CyuA |
| * | NC_000913 | 1,612,182 | 0 | T | C | 59.6% | 205.3 / inf | 260 | K48K (AAA→AAG) | yneG | conserved protein YneG |
| * | NC_000913 | 1,594,124 | 1 | . | C | 53.4% | 383.8 / inf | 174 | pseudogene (3963/5422 nt) | yneO | AIDA‑I family autotransporter YneO |
| * | NC_000913 | 4,602,103 | 0 | T | C | 39.4% | 212.2 / inf | 251 | L252L (CTA→CTG) | yjjP | putative succinate exporter YjjP |
| * | NC_000913 | 123,282 | 0 | A | G | 38.7% | 301.4 / inf | 310 | N89S (AAC→AGC) | aceE | pyruvate dehydrogenase E1 component |
| * | NC_000913 | 30,702 | 1 | . | G | 37.7% | 240.0 / inf | 236 | coding (1052/1149 nt) | carA | carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 574,384 | 0 | A | G | 36.6% | 350.6 / inf | 328 | intergenic (+45/+145) | ybcQ/nmpC | DLP12 prophage; putative antitermination protein/DLP12 prophage; putative outer membrane porin NmpC |
| * | NC_000913 | 2,228,490 | 0 | T | C | 36.3% | 363.0 / inf | 311 | pseudogene (269/1436 nt) | mdtQ | putative multidrug resistance outer membrane protein MdtQ |
| * | NC_000913 | 1,698,548 | 0 | A | . | 35.5% | 551.4 / 311.8 | 201 | coding (633/1029 nt) | malI | DNA‑binding transcriptional repressor MalI |
| * | NC_000913 | 3,415,324 | 0 | A | G | 33.1% | 433.1 / inf | 312 | T98A (ACC→GCC) | acrF | multidrug efflux pump RND permease AcrF |
| * | NC_000913 | 733,054 | 0 | A | G | 32.8% | 379.1 / 302.5 | 271 | I1158V (ATC→GTC) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 3,197,669 | 0 | A | G | 31.2% | 334.3 / 227.1 | 215 | V658A (GTT→GCT) | glnE | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
| * | NC_000913 | 3,022,566 | 0 | G | A | 30.8% | 468.5 / 283.6 | 286 | W417* (TGG→TGA) | xdhD | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.5% | 914.2 / inf | 505 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,479,581 | 0 | A | G | 29.6% | 702.1 / inf | 399 | intergenic (‑44/‑149) | yjgM/yjgN | putative acetyltransferase YjgM/conserved inner membrane protein YjgN |
| * | NC_000913 | 2,767,438 | 1 | . | C | 26.5% | 331.7 / 213.2 | 166 | intergenic (+83/‑272) | rnlB/yfjP | CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,761,780 | 0 | T | C | 26.5% | 476.4 / 197.0 | 242 | L4L (TTA→TTG) T245A (ACC→GCC) | sufD sufC | Fe‑S cluster scaffold complex subunit SufD Fe‑S cluster scaffold complex subunit SufC |
| * | NC_000913 | 1,879,355 | 0 | T | . | 22.3% | 883.8 / 258.4 | 283 | intergenic (‑100/+48) | yeaQ/yoaG | PF04226 family protein YeaQ/DUF1869 domain‑containing protein YoaG |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 202 (0.700) | 109 (0.450) | 80/162 | 4.7 | 42.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 125 (0.520) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1207790 = | 200 (0.690) | 107 (0.440) | 77/162 | 5.2 | 41.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 132 (0.550) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 71350 | 358 (1.240) | 102 (0.360) | 49/188 | 14.9 | 37.0% | intergenic (+85/‑1) | araC/yabI | DNA‑binding transcriptional dual regulator AraC/DedA family protein YabI |
| ? | NC_000913 | = 2857042 | 0 (0.000) | intergenic (‑236/‑51) | ygbA/mutS | protein YgbA/DNA mismatch repair protein MutS | |||||
| * | ? | NC_000913 | 4542682 = | 343 (1.190) | 56 (0.210) | 44/176 | 15.2 | 15.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 321 (1.220) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 327 (1.130) | 47 (0.180) | 38/176 | 17.3 | 13.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 314 (1.200) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1209618 | 178 (0.620) | 16 (0.070) | 12/164 | 28.9 | 7.4% | pseudogene (38/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment |
| ? | NC_000913 | 2471897 = | 251 (1.030) | pseudogene (166/519 nt) | yfdL | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL | |||||