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 | 31,941 | 0 | C | G | 57.2% | 155.4 / inf | 320 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 57.2% | 144.1 / inf | 320 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,939 | 0 | C | G | 57.0% | 121.2 / inf | 320 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 8,772 | 0 | A | C | 56.9% | 754.1 / inf | 347 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 8,770 | 0 | G | C | 56.8% | 122.5 / inf | 347 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 56.5% | 117.2 / inf | 347 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,221 | 0 | T | C | 45.9% | 246.9 / inf | 268 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | NC_000913 | 4,168,215 | 0 | A | T | 44.9% | 262.9 / inf | 256 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 31,938 | 0 | C | . | 43.3% | 683.2 / inf | 314 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 8,767 | 1 | . | C | 42.9% | 61.0 / inf | 347 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 31,941 | 1 | . | G | 42.5% | 76.9 / inf | 320 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | NC_000913 | 4,168,472 | 0 | G | A | 29.3% | 310.1 / 169.7 | 191 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,475 | 0 | G | T | 28.0% | 367.3 / 177.2 | 186 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 28.0% | 325.5 / 158.1 | 186 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | BN000925 | 38,390 | 1 | . | G | 22.2% | 904.2 / inf | 374 | pseudogene (47/171 nt) | upf35.8 | probable truncation of theoretical product due to sequence errors |
| Marginal new junction evidence (lowest skew 10 of 30 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 141 (1.280) | 24 (0.240) | 21/398 | 4.0 | 17.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 90 (0.880) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1207790 = | 147 (1.330) | 19 (0.190) | 18/398 | 4.6 | 14.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 92 (0.900) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 17 (0.160) | 13/412 | 6.0 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 3817697 = | 108 (0.980) | 9 (0.080) | 8/414 | 7.7 | 8.1% | intergenic (+158/‑63) | yicC/dinD | UPF0701 family protein YicC/DNA damage‑inducible protein D |
| ? | NC_000913 | 3817717 = | 101 (0.950) | intergenic (+178/‑43) | yicC/dinD | UPF0701 family protein YicC/DNA damage‑inducible protein D | |||||
| * | ? | NC_000913 | 457316 = | 126 (1.140) | 5 (0.050) | 5/414 | 9.1 | 3.9% | intergenic (+16/‑110) | clpP/clpX | ATP‑dependent Clp protease proteolytic subunit/ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| ? | NC_000913 | 457346 = | 122 (1.150) | intergenic (+46/‑80) | clpP/clpX | ATP‑dependent Clp protease proteolytic subunit/ATP‑dependent Clp protease ATP‑binding subunit ClpX | |||||
| * | ? | NC_000913 | 2765420 = | 135 (1.220) | 3 (0.030) | 3/342 | 9.2 | 2.8% | intergenic (‑267/+93) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| ? | NC_000913 | = 2765411 | 104 (1.190) | intergenic (‑258/+102) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM | |||||
| * | ? | NC_000913 | = 1209618 | 94 (0.850) | 4 (0.040) | 4/400 | 9.5 | 4.0% | pseudogene (38/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment |
| ? | NC_000913 | 2471897 = | 105 (1.020) | pseudogene (166/519 nt) | yfdL | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL | |||||
| * | ? | NC_000913 | = 3620868 | NA (NA) | 4 (0.040) | 4/408 | 9.6 | 3.9% | coding (1677/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3621008 | 103 (0.930) | coding (1817/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 1205780 = | 107 (0.970) | 4 (0.040) | 4/416 | 9.7 | 3.8% | coding (50/474 nt) | beeE | e14 prophage; putative protein BeeE |
| ? | NC_000913 | 1205797 = | 100 (0.940) | coding (67/474 nt) | beeE | e14 prophage; putative protein BeeE | |||||
| * | ? | NC_000913 | 550555 = | 87 (0.790) | 4 (0.040) | 4/414 | 9.7 | 4.4% | coding (117/894 nt) | ybcF | putative carbamate kinase |
| ? | NC_000913 | 550597 = | 91 (0.860) | coding (159/894 nt) | ybcF | putative carbamate kinase | |||||