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 251 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 339,986 | 0 | G | A | 75.0% | 34.2 / 16.4 | 28 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,979 | 0 | G | A | 69.0% | 24.0 / 19.6 | 29 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 1,634,382 | 0 | T | C | 63.3% | ‑4.8 / 31.1 | 30 | K168K (AAA→AAG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,597 | 0 | C | A | 62.4% | ‑1.4 / 202.1 | 171 | V97F (GTT→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,578 | 0 | T | C | 61.6% | 2.3 / 200.5 | 164 | E103G (GAA→GGA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,699 | 0 | A | C | 61.6% | 2.0 / 174.0 | 151 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,724 | 0 | G | A | 61.2% | 6.6 / 142.7 | 135 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,404 | 0 | A | G | 61.0% | ‑4.7 / 41.3 | 41 | I161T (ATC→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,676 | 0 | A | G | 61.0% | ‑2.7 / 200.4 | 164 | D70D (GAT→GAC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,484 | 0 | G | T | 60.8% | ‑2.4 / 116.7 | 97 | N134K (AAC→AAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,661 | 0 | C | G | 60.5% | ‑3.0 / 232.3 | 172 | T75T (ACG→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,482 | 0 | T | C | 60.4% | ‑1.1 / 112.4 | 97 | N135S (AAC→AGC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,569 | 0 | A | T | 60.3% | 8.4 / 245.4 | 152 | F106Y (TTT→TAT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,388 | 0 | T | G | 60.0% | ‑5.1 / 37.9 | 35 | A166A (GCA→GCC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,571 | 0 | C | T | 59.5% | 3.5 / 190.8 | 153 | E105E (GAG→GAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,658 | 0 | A | G | 59.1% | 5.7 / 229.6 | 176 | V76V (GTT→GTC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 580,115 | 0 | C | T | 54.6% | 120.2 / inf | 252 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 579,099 | 0 | A | . | 54.3% | 18.9 / inf | 283 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,127 | 0 | T | C | 54.0% | 63.4 / inf | 264 | intergenic (‑234/+57) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,769 | 0 | T | A | 53.6% | 42.3 / 212.9 | 112 | P39P (CCA→CCT) | tfaQ | putative tail fiber assembly protein TfaQ |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 173 (1.690) | 26 (0.260) | 24/580 | 3.3 | 13.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 160 (1.610) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 566774 | 104 (1.010) | 48 (0.470) | 22/594 | 3.7 | 31.0% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 110 (1.080) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 4542690 | 183 (1.790) | 23 (0.230) | 21/580 | 3.8 | 12.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 158 (1.590) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1096961 = | 72 (0.700) | 8 (0.110) | 6/438 | 6.7 | 12.7% | intergenic (+132/+604) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 57 (0.760) | intergenic (+674/+62) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 1287463 | 0 (0.000) | 17 (0.170) | 9/586 | 7.1 | 100% | intergenic (‑135/+75) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287574 = | 0 (0.000) | noncoding (49/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 3648146 | 121 (1.180) | 8 (0.100) | 6/482 | 7.3 | 7.3% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 105 (1.270) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | 1411899 = | 122 (1.190) | 6 (0.060) | 6/546 | 8.0 | 4.7% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 131 (1.400) | intergenic (‑552/+227) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | 2818197 = | 36 (0.350) | 3 (0.040) | 3/440 | 8.5 | 6.6% | intergenic (‑62/+1) | argZ/argY | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | = 2818471 | 59 (0.780) | intergenic (‑197/+2) | argY/argV | tRNA‑Arg/tRNA‑Arg | |||||
| * | ? | NC_000913 | = 781688 | 84 (0.820) | 4 (0.050) | 4/490 | 8.5 | 5.2% | intergenic (+36/‑397) | lysQ/nadA | tRNA‑Lys/quinolinate synthase |
| ? | NC_000913 | 781845 = | 77 (0.920) | intergenic (+193/‑240) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4206106 | 121 (1.180) | 4 (0.040) | 4/580 | 9.4 | 3.1% | coding (1427/1590 nt) | purH | bifunctional AICAR transformylase/IMP cyclohydrolase |
| ? | NC_000913 | 4206448 = | 131 (1.320) | coding (1085/1590 nt) | purH | bifunctional AICAR transformylase/IMP cyclohydrolase | |||||