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 | 31,939 | 0 | C | G | 64.4% | 523.9 / inf | 493 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 0 | C | G | 64.4% | 538.3 / inf | 493 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 64.2% | 524.7 / inf | 493 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 8,770 | 0 | G | C | 57.3% | 222.2 / inf | 521 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,772 | 0 | A | C | 57.3% | inf / inf | 521 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 57.2% | 222.9 / inf | 521 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,221 | 0 | T | C | 44.2% | 288.6 / inf | 292 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | NC_000913 | 4,168,215 | 0 | A | T | 42.4% | 330.0 / inf | 290 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 8,767 | 1 | . | C | 41.9% | 148.3 / inf | 521 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 31,938 | 0 | C | . | 35.2% | 1226.2 / inf | 491 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 1 | . | G | 35.1% | 500.6 / inf | 493 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | NC_000913 | 4,168,472 | 0 | G | A | 30.5% | 230.5 / 154.9 | 167 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,475 | 0 | G | T | 28.7% | 266.6 / 158.1 | 160 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 28.6% | 251.5 / 136.8 | 161 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| Marginal new junction evidence (lowest skew 10 of 39 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 115 (1.070) | 26 (0.260) | 23/396 | 3.3 | 19.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 109 (1.090) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 111 (1.030) | 19 (0.190) | 17/396 | 4.4 | 15.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 102 (1.020) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 8 (0.080) | 8/410 | 7.2 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2286126 = | 115 (1.070) | 6 (0.060) | 6/402 | 7.9 | 5.2% | coding (1751/1761 nt) | yejM | putative cardiolipin transport protein |
| ? | NC_000913 | 2286159 = | 110 (1.090) | intergenic (+23/‑52) | yejM/proL | putative cardiolipin transport protein/tRNA‑Pro | |||||
| * | ? | NC_000913 | 1430276 = | 75 (0.700) | 7 (0.070) | 6/410 | 8.0 | 7.5% | coding (1228/3363 nt) | stfR | Rac prophage; putative membrane protein |
| ? | NC_000913 | 1430422 = | 100 (0.970) | coding (1374/3363 nt) | stfR | Rac prophage; putative membrane protein | |||||
| * | ? | NC_000913 | = 4373269 | NA (NA) | 7 (0.070) | 6/416 | 8.1 | NA | noncoding (28/34 nt) | other | REP328b |
| ? | NC_000913 | 4374576 = | NA (NA) | noncoding (22/29 nt) | other | REPv329b | |||||
| * | ? | NC_000913 | = 4542690 | 118 (1.100) | 7 (0.070) | 5/410 | 8.5 | 6.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 103 (1.000) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3880655 | 143 (1.330) | 6 (0.060) | 5/408 | 8.5 | 4.3% | coding (567/1074 nt) | recF | DNA repair protein RecF |
| ? | NC_000913 | = 3880717 | 129 (1.260) | coding (505/1074 nt) | recF | DNA repair protein RecF | |||||
| * | ? | NC_000913 | = 1209618 | 111 (1.030) | 6 (0.060) | 4/398 | 8.9 | 5.4% | pseudogene (38/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment |
| ? | NC_000913 | 2471897 = | 109 (1.090) | pseudogene (166/519 nt) | yfdL | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL | |||||
| * | ? | NC_000913 | 716906 = | 104 (0.970) | 4 (0.040) | 4/408 | 9.0 | 3.8% | intergenic (‑309/+40) | ybfG/potE | PF10964 domain‑containing protein YbfG/putrescine:H(+) symporter/putrescine:ornithine antiporter PotE |
| ? | NC_000913 | 716932 = | 106 (1.030) | intergenic (‑335/+14) | ybfG/potE | PF10964 domain‑containing protein YbfG/putrescine:H(+) symporter/putrescine:ornithine antiporter PotE | |||||