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 | 64.3% | 350.0 / inf | 310 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,939 | 0 | C | G | 64.1% | 341.4 / inf | 309 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 63.9% | 341.2 / inf | 310 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 8,772 | 0 | A | C | 60.7% | 896.8 / inf | 385 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 60.5% | 291.9 / inf | 385 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,770 | 0 | G | C | 60.2% | 276.7 / inf | 385 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,221 | 0 | T | C | 46.5% | 274.2 / inf | 318 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | NC_000913 | 4,168,215 | 0 | A | T | 45.6% | 293.5 / inf | 316 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 8,767 | 1 | . | C | 39.2% | 221.9 / inf | 385 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 31,938 | 0 | C | . | 35.7% | 768.5 / inf | 305 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 1 | . | G | 35.5% | 309.7 / inf | 310 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | NC_000913 | 4,168,472 | 0 | G | A | 30.4% | 369.8 / 231.0 | 247 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,475 | 0 | G | T | 29.9% | 418.3 / 252.3 | 244 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 29.9% | 383.6 / 226.3 | 245 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| Marginal new junction evidence (lowest skew 10 of 36 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 807336 | 0 (0.000) | 99 (0.690) +G |
40/430 | 3.0 | 57.8% | intergenic (‑55/+97) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | = 4171849 | 145 (1.010) | intergenic (+93/‑208) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | 1207790 = | 146 (1.010) | 42 (0.320) | 35/400 | 3.2 | 25.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 110 (0.830) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 151 (1.050) | 37 (0.280) | 30/400 | 4.0 | 23.1% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 106 (0.800) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 807336 | 0 (0.000) | 53 (0.370) +G |
26/430 | 5.1 | 43.2% | intergenic (‑55/+97) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | = 4040729 | 140 (0.970) | intergenic (+93/+177) | rrfA/mobB | 5S ribosomal RNA/molybdopterin‑guanine dinucleotide biosynthesis adaptor protein | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 20 (0.140) | 15/414 | 7.6 | 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) | 27 (0.190) +G |
11/430 | 9.2 | 29.1% | intergenic (‑55/+97) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | 3423330 = | 132 (0.920) | intergenic (+136/+93) | yhdZ/rrfF | putative ABC transporter ATP‑binding subunit YhdZ/5S ribosomal RNA | |||||
| * | ? | NC_000913 | 1560067 = | 2046 (14.200) | 13 (0.090) | 10/414 | 9.3 | 0.66% | coding (863/1023 nt) | ddpB | putative D,D‑dipeptide ABC transporter membrane subunit DdpB |
| ? | NC_000913 | 1560214 = | 1963 (14.220) | coding (716/1023 nt) | ddpB | putative D,D‑dipeptide ABC transporter membrane subunit DdpB | |||||
| * | ? | NC_000913 | 1430276 = | 102 (0.710) | 12 (0.090) | 10/414 | 9.3 | 10.2% | coding (1228/3363 nt) | stfR | Rac prophage; putative membrane protein |
| ? | NC_000913 | 1430422 = | 113 (0.820) | coding (1374/3363 nt) | stfR | Rac prophage; putative membrane protein | |||||
| * | ? | NC_000913 | 1560795 = | 1798 (12.480) | 10 (0.070) | 9/416 | 9.8 | 0.57% | coding (135/1023 nt) | ddpB | putative D,D‑dipeptide ABC transporter membrane subunit DdpB |
| ? | NC_000913 | 1560823 = | 1744 (12.580) | coding (107/1023 nt) | ddpB | putative D,D‑dipeptide ABC transporter membrane subunit DdpB | |||||
| * | ? | NC_000913 | = 2713829 | 181 (1.260) | 3 (0.030) +79 bp |
3/274 | 10.3 | 2.7% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase SrmB |
| ? | NC_000913 | 2713909 = | 167 (1.160) | coding (1014/1335 nt) | srmB | ATP‑dependent RNA helicase SrmB | |||||