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 292 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 811,531 | 0 | G | A | 78.2% | 199.5 / 55.0 | 102 | G384D (GGT→GAT) V4I (GTT→ATT) | bioF bioC | 8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| * | NC_000913 | 715,765 | 0 | C | T | 76.9% | 68.8 / 18.7 | 39 | P118P (CCC→CCT) | ybfP | lipoprotein YbfP |
| * | NC_000913 | 3,554,160 | 0 | A | G | 75.4% | 112.3 / 36.1 | 65 | E359G (GAA→GGA) | malT | DNA‑binding transcriptional activator MalT |
| * | NC_000913 | 4,566,642 | 0 | G | A | 74.7% | 152.9 / 53.6 | 83 | S202L (TCG→TTG) | yjiN | DUF445 domain‑containing protein YjiN |
| * | NC_000913 | 579,385 | 0 | A | G | 61.1% | 27.3 / 63.2 | 54 | N70N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,778 | 0 | T | G | 56.2% | ‑0.9 / 32.9 | 32 | T36T (ACA→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,429,111 | 0 | A | C | 54.8% | 53.7 / 103.9 | 84 | T21T (ACA→ACC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 579,457 | 0 | A | G | 53.7% | 1.6 / 74.7 | 54 | I46I (ATT→ATC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,429,114 | 0 | C | T | 53.5% | 24.6 / 116.2 | 86 | I22I (ATC→ATT) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 579,540 | 0 | T | C | 53.4% | 4.5 / 82.3 | 58 | N19D (AAC→GAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,769 | 0 | T | A | 52.9% | 5.9 / 51.0 | 34 | P39P (CCA→CCT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,502 | 0 | A | G | 52.5% | 0.8 / 85.5 | 59 | N31N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,429,128 | 0 | A | G | 52.1% | 25.1 / 125.9 | 94 | K27R (AAA→AGA) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,171 | 0 | A | G | 51.4% | 7.7 / 152.8 | 105 | E41E (GAA→GAG) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,126 | 0 | A | C | 51.1% | 19.5 / 131.2 | 94 | A26A (GCA→GCC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,160 | 0 | C | G | 51.0% | 28.4 / 161.4 | 97 | L38V (CTG→GTG) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 579,271 | 0 | G | A | 50.8% | ‑2.9 / 90.6 | 59 | H108H (CAC→CAT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,099 | 0 | A | . | 50.0% | 76.5 / 90.8 | 50 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,127 | 0 | T | C | 50.0% | ‑4.4 / 64.2 | 47 | intergenic (‑234/+57) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,097,494 | 0 | T | A | 50.0% | ‑6.4 / 41.7 | 32 | intergenic (+665/+71) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| Marginal new junction evidence (lowest skew 10 of 51 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 2514274 = | NA (NA) | 13 (0.230) | 13/480 | 2.4 | 18.3% | noncoding (2/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 2955099 | 58 (1.030) | coding (905/3543 nt) | recB | exodeoxyribonuclease V subunit RecB | |||||
| * | ? | NC_000913 | 1979271 = | 1 (0.020) | 9 (0.170) +TTAAGTAATTGAGTG |
9/456 | 3.0 | 90.6% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | 2996360 = | NA (NA) | intergenic (+2504/+12) | ygeI/insD4 | protein YgeI/IS2 insertion element protein InsB | |||||
| * | ? | NC_000913 | = 2997694 | NA (NA) | 9 (0.160) +C |
9/484 | 3.2 | NA | intergenic (‑94/+340) | insC4/ygeQ | IS2 insertion element repressor InsA/putative lipoprotein YgeQ |
| ? | NC_000913 | = 3187427 | NA (NA) | intergenic (+12/‑5) | insD5/yqiG | IS2 insertion element protein InsB/putative outer membrane usher protein YqiG | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 10 (0.180) | 9/484 | 3.2 | 28.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3131469 = | 25 (0.440) | coding (940/1068 nt) | yghQ | putative transport protein YghQ | |||||
| * | ? | NC_000913 | = 1469245 | NA (NA) | 9 (0.160) | 9/486 | 3.2 | NA | intergenic (‑96/‑1) | insC2/ydbA | IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | = 1651548 | NA (NA) | noncoding (706/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1467905 = | NA (NA) | 9 (0.160) | 9/486 | 3.2 | NA | pseudogene (2514/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | = 2070271 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 290634 = | NA (NA) | 9 (0.160) | 9/486 | 3.2 | 20.9% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1105699 = | 34 (0.600) | coding (286/312 nt) | ymdA | uncharacterized protein YmdA | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 10 (0.180) | 9/486 | 3.2 | 28.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 481058 | 25 (0.440) | intergenic (‑350/+196) | tomB/acrB | Hha toxicity modulator TomB/multidrug efflux pump RND permease AcrB | |||||
| * | ? | NC_000913 | = 1411924 | 28 (0.490) | 8 (0.160) | 7/434 | 3.3 | 27.1% | coding (25/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | 1434985 = | 18 (0.350) | intergenic (‑579/+200) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 8 (0.140) | 8/486 | 3.4 | 17.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3655259 = | 37 (0.650) | coding (644/648 nt) | yhiD | inner membrane protein YhiD | |||||