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 | ||
| * | BN000925 | 8,772 | 0 | A | C | 61.8% | 805.6 / inf | 349 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 8,770 | 0 | G | C | 61.6% | 296.3 / inf | 349 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 61.6% | 275.2 / inf | 349 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 31,939 | 0 | C | G | 59.0% | 175.0 / inf | 285 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 58.3% | 176.7 / inf | 288 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 0 | C | G | 58.3% | 163.2 / inf | 288 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 1 | . | G | 41.7% | 87.2 / inf | 288 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,938 | 0 | C | . | 41.3% | 638.6 / inf | 283 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | NC_000913 | 4,168,221 | 0 | T | C | 41.1% | 188.4 / 206.9 | 163 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | NC_000913 | 4,168,215 | 0 | A | T | 39.6% | 203.6 / 234.2 | 169 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 8,767 | 1 | . | C | 38.4% | 219.8 / inf | 349 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,472 | 0 | G | A | 35.2% | 91.7 / 96.3 | 91 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,475 | 0 | G | T | 32.2% | 126.5 / 95.4 | 90 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 32.2% | 116.9 / 83.1 | 90 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 1,466,210 | 0 | G | A | 23.9% | 81.0 / 22.5 | 46 | pseudogene (819/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.0% | 198.9 / 66.5 | 100 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,466,201 | 0 | T | C | 20.4% | 104.7 / 18.2 | 49 | pseudogene (810/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381292 = | NA (NA) | 15 (0.240) | 13/408 | 3.3 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 4542682 = | 69 (1.050) | 9 (0.140) | 9/408 | 4.3 | 12.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 59 (0.930) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 63 (0.960) | 5 (0.080) | 5/408 | 5.7 | 7.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 59 (0.930) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 3232456 = | 68 (1.030) | 5 (0.080) | 5/410 | 5.7 | 8.1% | coding (792/2019 nt) | fadH | 2,4‑dienoyl‑CoA reductase |
| ? | NC_000913 | 3232574 = | 48 (0.760) | coding (910/2019 nt) | fadH | 2,4‑dienoyl‑CoA reductase | |||||
| * | ? | NC_000913 | = 4055722 | 66 (1.000) | 5 (0.080) | 4/410 | 6.2 | 7.1% | coding (618/1050 nt) | glnL | sensory histidine kinase NtrB |
| ? | NC_000913 | = 4055751 | 67 (1.060) | coding (589/1050 nt) | glnL | sensory histidine kinase NtrB | |||||
| * | ? | NC_000913 | = 2170358 | 10 (0.150) | 3 (0.050) | 3/400 | 6.6 | 24.2% | noncoding (188/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 2170558 | NA (NA) | noncoding (388/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1095115 = | NA (NA) | 3 (0.050) | 3/400 | 6.6 | 24.2% | noncoding (388/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 1095315 = | 10 (0.150) | noncoding (188/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 566964 | 6 (0.090) | 3 (0.050) | 3/400 | 6.6 | 34.8% | noncoding (188/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 567164 | NA (NA) | noncoding (388/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 392579 = | NA (NA) | 3 (0.050) | 3/400 | 6.6 | 13.8% | noncoding (388/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 392779 = | 20 (0.300) | noncoding (188/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315413 | 10 (0.150) | 3 (0.050) | 3/400 | 6.6 | 24.2% | noncoding (185/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315613 | NA (NA) | noncoding (385/1255 nt) | IS3 | repeat region | |||||