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 | 8,770 | 0 | G | C | 58.9% | 248.2 / inf | 455 | A457P (GCA→CCA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,771 | 0 | C | G | 58.9% | 247.5 / inf | 455 | A457G (GCA→GGA) ‡ | tnpA | Tn1 transposase |
| * | BN000925 | 8,772 | 0 | A | C | 58.7% | inf / inf | 455 | coding (1371/3006 nt) | tnpA | Tn1 transposase |
| * | BN000925 | 31,939 | 0 | C | G | 58.5% | 181.2 / inf | 378 | P88R (CCG→CGG) ‡ | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 0 | C | G | 58.4% | 185.3 / inf | 379 | P89A (CCT→GCT) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,940 | 0 | G | C | 58.3% | 177.8 / inf | 379 | P88P (CCG→CCC) ‡ | upf31.7 | hypothetical protein |
| * | NC_000913 | 4,168,221 | 0 | T | C | 45.6% | 230.2 / inf | 237 | intergenic (+21/‑151) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | NC_000913 | 4,168,215 | 0 | A | T | 44.7% | 245.3 / inf | 235 | intergenic (+15/‑157) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| * | BN000925 | 31,938 | 0 | C | . | 41.7% | 856.7 / inf | 372 | coding (262/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 31,941 | 1 | . | G | 41.2% | 143.8 / inf | 379 | coding (265/420 nt) | upf31.7 | hypothetical protein |
| * | BN000925 | 8,767 | 1 | . | C | 41.1% | 170.2 / inf | 455 | coding (1366/3006 nt) | tnpA | Tn1 transposase |
| * | NC_000913 | 4,168,472 | 0 | G | A | 29.4% | 245.6 / 137.2 | 153 | intergenic (+25/‑169) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,475 | 0 | G | T | 26.7% | 293.5 / 131.0 | 146 | intergenic (+28/‑166) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 4,168,476 | 0 | A | G | 26.7% | 270.9 / 115.7 | 146 | intergenic (+29/‑165) | gltT/rrlB | tRNA‑Glu/23S ribosomal RNA |
| * | BN000925 | 38,390 | 1 | . | G | 20.4% | 1270.4 / inf | 496 | pseudogene (47/171 nt) | upf35.8 | probable truncation of theoretical product due to sequence errors |
| 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 | 381292 = | NA (NA) | 18 (0.210) | 13/414 | 4.6 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2765420 = | 128 (1.410) | 4 (0.060) | 3/344 | 7.6 | 4.0% | intergenic (‑267/+93) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| ? | NC_000913 | = 2765411 | 89 (1.230) | intergenic (‑258/+102) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM | |||||
| * | ? | NC_000913 | 285962 = | 75 (0.830) | 4 (0.050) | 4/408 | 7.8 | 4.8% | coding (568/1383 nt) | yagG | putative D‑xylonate transporter YagG |
| ? | NC_000913 | 286405 = | 89 (1.040) | coding (1011/1383 nt) | yagG | putative D‑xylonate transporter YagG | |||||
| * | ? | NC_000913 | 1045201 = | 101 (1.110) | 4 (0.050) | 4/414 | 7.9 | 3.9% | coding (603/1140 nt) | gfcE | putative exopolysaccharide export lipoprotein GfcE |
| ? | NC_000913 | 1045310 = | 103 (1.180) | coding (494/1140 nt) | gfcE | putative exopolysaccharide export lipoprotein GfcE | |||||
| * | ? | NC_000913 | = 374417 | 79 (0.870) | 4 (0.050) | 4/416 | 7.9 | 5.5% | coding (550/1014 nt) | mhpE | 4‑hydroxy‑2‑oxovalerate aldolase |
| ? | NC_000913 | = 374547 | 62 (0.710) | coding (680/1014 nt) | mhpE | 4‑hydroxy‑2‑oxovalerate aldolase | |||||
| * | ? | NC_000913 | 1411899 = | 103 (1.130) | 3 (0.040) | 3/380 | 8.0 | 3.3% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 86 (1.080) | pseudogene (51/51 nt) | ttcC | putative tRNA 2‑thiocytidine (s(2)C32) synthase | |||||
| * | ? | NC_000913 | 1703236 = | 98 (1.080) | 3 (0.040) | 3/402 | 8.3 | 3.3% | intergenic (+2/+32) | add/ydgJ | adenosine deaminase/putative oxidoreductase YdgJ |
| ? | NC_000913 | 1703268 = | 85 (1.010) | coding (1041/1041 nt) | ydgJ | putative oxidoreductase YdgJ | |||||
| * | ? | NC_000913 | 4542682 = | 73 (0.800) | 3 (0.030) | 3/414 | 8.4 | 4.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 69 (0.790) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3858205 | 95 (1.050) | 4 (0.050) | 3/406 | 8.4 | 4.9% | coding (200/1494 nt) | yidJ | putative sulfatase/phosphatase |
| ? | NC_000913 | = 3858228 | 65 (0.760) | coding (177/1494 nt) | yidJ | putative sulfatase/phosphatase | |||||
| * | ? | NC_000913 | = 2647282 | 70 (0.770) | 3 (0.030) | 3/412 | 8.4 | 4.7% | coding (44/2313 nt) | pbpC | peptidoglycan glycosyltransferase PbpC |
| ? | NC_000913 | = 2647351 | 54 (0.620) | coding (4937/4962 nt) | yfhM | alpha2‑macroglobulin | |||||