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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 952,460 | 0 | A | C | 68.8% | 317.2 / 191.1 | 177 | G365G (GGT→GGG) | pflB | pyruvate formate‑lyase |
| * | BN000925 | 31,939 | 0 | C | G | 61.3% | 350.1 / inf | 466 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 61.2% | 358.0 / inf | 467 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 0 | C | G | 61.2% | 361.6 / inf | 467 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 8,772 | 0 | A | C | 57.9% | inf / inf | 581 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 57.8% | 262.8 / inf | 581 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,770 | 0 | G | C | 57.7% | 261.3 / inf | 581 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,221 | 0 | T | C | 43.8% | 382.1 / inf | 348 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | NC_000913 | 4,168,215 | 0 | A | T | 42.2% | 417.7 / inf | 346 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 8,767 | 1 | . | C | 42.2% | 150.1 / inf | 581 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 31,938 | 0 | C | . | 38.9% | 1097.4 / inf | 463 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 1 | . | G | 38.8% | 304.3 / inf | 467 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | NC_000913 | 1,204,463 | 0 | G | T | 35.0% | 240.6 / 198.1 | 163 | A98A (GCG→GCT) pseudogene (63/1137 nt) | ymfN aaaE | e14 prophage; chimeric replication protein/phage terminase YmfN phage terminase |
| * | NC_000913 | 4,168,472 | 0 | G | A | 28.1% | 416.8 / 221.0 | 256 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,475 | 0 | G | T | 27.0% | 478.4 / 232.5 | 252 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 26.8% | 442.6 / 204.5 | 251 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | BN000925 | 38,390 | 1 | . | G | 20.5% | 1558.8 / inf | 604 | pseudogene (47/171 nt) | upf35.8 | probable truncation of theoretical product due to sequence errors |
| Marginal new junction evidence (lowest skew 10 of 41 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 807336 | 0 (0.000) | 82 (0.600) +G |
35/430 | 3.1 | 53.7% | intergenic (‑55/+97) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | = 4171849 | 142 (1.030) | intergenic (+93/‑208) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | = 1207805 | 166 (1.210) | 31 (0.240) | 26/400 | 4.0 | 20.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 84 (0.660) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1207790 = | 156 (1.130) | 36 (0.280) | 25/400 | 4.2 | 23.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 85 (0.670) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 807336 | 0 (0.000) | 38 (0.280) +G |
22/430 | 5.1 | 36.6% | intergenic (‑55/+97) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | = 4040729 | 132 (0.960) | intergenic (+93/+177) | rrfA/mobB | 5S ribosomal RNA/molybdopterin‑guanine dinucleotide biosynthesis adaptor protein | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 14 (0.110) | 9/414 | 8.5 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 807336 | 0 (0.000) | 14 (0.100) +G |
9/430 | 8.8 | 18.5% | intergenic (‑55/+97) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | 3423330 = | 124 (0.900) | intergenic (+136/+93) | yhdZ/rrfF | putative ABC transporter ATP‑binding subunit YhdZ/5S ribosomal RNA | |||||
| * | ? | NC_000913 | = 4542690 | 113 (0.820) | 6 (0.050) | 5/414 | 10.4 | 5.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 116 (0.880) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 447217 = | 186 (1.350) | 4 (0.030) | 4/410 | 10.9 | 2.3% | coding (489/891 nt) | cyoE | heme O synthase |
| ? | NC_000913 | 447278 = | 158 (1.210) | coding (428/891 nt) | cyoE | heme O synthase | |||||
| * | ? | NC_000913 | = 3686344 | 150 (1.090) | 6 (0.050) | 4/412 | 11.0 | 3.9% | coding (2830/3474 nt) | bcsC | cellulose biosynthesis protein BcsC |
| ? | NC_000913 | = 3686424 | 149 (1.140) | coding (2750/3474 nt) | bcsC | cellulose biosynthesis protein BcsC | |||||
| * | ? | NC_000913 | 3220520 = | 114 (0.830) | 4 (0.030) | 4/414 | 11.0 | 3.1% | coding (1027/1380 nt) | patA | putrescine aminotransferase |
| ? | NC_000913 | 3220730 = | 143 (1.080) | coding (1237/1380 nt) | patA | putrescine aminotransferase | |||||