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 44 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,509,586 | 0 | A | C | 50.0% | 18.2 / 207.0 | 176 | pseudogene (108/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,487 | 0 | A | G | 44.0% | 52.9 / 213.2 | 168 | pseudogene (9/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,416 | 0 | T | C | 43.4% | 67.0 / 210.3 | 173 | pseudogene (408/471 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,428 | 0 | A | G | 43.2% | 74.5 / 196.4 | 169 | pseudogene (420/471 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,544 | 0 | G | A | 43.1% | 87.2 / 205.7 | 175 | pseudogene (66/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,537 | 0 | G | A | 42.9% | 72.5 / 204.6 | 175 | pseudogene (59/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,037,496 | 0 | A | T | 42.4% | 109.7 / 234.7 | 151 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 4,509,463 | 0 | T | G | 42.2% | 61.9 / 225.1 | 174 | pseudogene (455/471 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,524 | 0 | C | T | 42.1% | 91.9 / 205.6 | 178 | pseudogene (46/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,556 | 0 | T | C | 41.2% | 87.9 / 195.1 | 170 | pseudogene (78/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,562 | 0 | T | C | 41.0% | 86.4 / 195.3 | 173 | pseudogene (84/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,478 | 1 | . | C | 40.9% | 110.6 / inf | 171 | pseudogene (470/471 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,592 | 0 | G | A | 38.4% | 139.7 / 174.9 | 172 | pseudogene (114/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 2,246,779 | 0 | C | A | 36.3% | 130.8 / 12.8 | 102 | intergenic (‑10/+284) | cirA/lysP | iron‑catecholate outer membrane transporter CirA/lysine:H(+) symporter |
| * | NC_000913 | 4,509,623 | 0 | G | A | 35.6% | 164.7 / 147.1 | 160 | pseudogene (145/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 2,990,480 | 0 | C | A | 33.1% | 186.8 / 16.5 | 124 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 4,360,965 | 0 | C | A | 32.6% | 254.4 / 24.6 | 144 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 3,054,894 | 0 | G | T | 31.8% | 101.0 / 13.4 | 66 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 4,509,628 | 0 | A | G | 31.3% | 186.9 / 123.4 | 150 | pseudogene (150/315 nt) | insO | IS911B regulator fragment |
| * | NC_000913 | 4,509,630 | 0 | C | T | 31.1% | 203.6 / 115.9 | 151 | pseudogene (152/315 nt) | insO | IS911B regulator fragment |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4094350 | 71 (0.830) | 11 (0.150) | 11/508 | 3.9 | 16.7% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094719 = | 49 (0.670) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 4606166 | 85 (0.990) | 7 (0.120) | 7/412 | 4.2 | 11.0% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 54 (0.900) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 696469 | 56 (0.650) | 18 (0.210) +TAGAAT |
12/578 | 4.2 | 26.3% | noncoding (36/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696802 = | 47 (0.550) | noncoding (29/75 nt) | glnW | tRNA‑Gln | |||||
| * | ? | NC_000913 | = 2947467 | 65 (0.760) | 7 (0.110) | 7/424 | 4.4 | 12.7% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 50 (0.810) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 1286906 | 48 (0.560) | 14 (0.180) | 9/550 | 4.8 | 25.1% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 39 (0.490) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 781222 | 56 (0.650) | 8 (0.130) | 6/438 | 4.9 | 16.9% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 37 (0.580) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 2818275 | 48 (0.560) | 5 (0.080) | 5/432 | 5.2 | 11.3% | intergenic (‑1/+198) | argY/argV | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818551 = | 43 (0.690) | intergenic (‑2/+2) | argV/serV | tRNA‑Arg/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 2653419 | 71 (0.830) | 10 (0.130) | 7/540 | 5.4 | 13.6% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 62 (0.790) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | 781369 = | 45 (0.530) | 10 (0.120) +GG |
8/586 | 5.4 | 14.8% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 71 (0.830) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 1287084 | 59 (0.690) | 7 (0.090) | 7/550 | 5.5 | 13.0% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 39 (0.490) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||