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 | ||
| * | NC_000913_3_bme_pgi | 2,755,880 | 0 | G | A | 31.2% | 1288.4 / inf | 929 | intergenic (+502/‑279) | smpB/intA | tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase |
| * | NC_000913_3_bme_pgi | 4,296,061 | 0 | C | T | 28.1% | 433.3 / 205.6 | 302 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_bme_pgi | 2,767,667 | 0 | T | G | 24.8% | 398.4 / 161.8 | 219 | intergenic (+312/‑43) | rnlB/yfjP | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; 50S ribosome‑binding GTPase family protein |
| * | NC_000913_3_bme_pgi | 2,767,670 | 0 | C | A | 24.2% | 445.4 / 147.6 | 216 | intergenic (+315/‑40) | rnlB/yfjP | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; 50S ribosome‑binding GTPase family protein |
| * | NC_000913_3_bme_pgi | 526,796 | 0 | C | G | 23.2% | 676.4 / 173.5 | 250 | A1179G (GCG→GGG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_bme_pgi | 526,792 | 0 | A | C | 22.9% | 613.2 / 175.2 | 262 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_bme_pgi | 1,778,364 | 0 | C | T | 22.4% | 398.9 / 112.9 | 206 | intergenic (+17/+26) | ydiO/ydiP | putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator |
| * | NC_000913_3_bme_pgi | 1,778,367 | 0 | C | G | 22.3% | 442.4 / 143.7 | 206 | intergenic (+20/+23) | ydiO/ydiP | putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator |
| * | NC_000913_3_bme_pgi | 1,778,375 | 0 | A | G | 21.0% | 420.5 / 117.2 | 214 | intergenic (+28/+15) | ydiO/ydiP | putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator |
| * | NC_000913_3_bme_pgi | 1,778,372 | 0 | C | G | 21.0% | 500.9 / 137.0 | 219 | intergenic (+25/+18) | ydiO/ydiP | putative acyl‑CoA dehydrogenase/putative DNA‑binding transcriptional regulator |
| * | NC_000913_3_bme_pgi | 526,800 | 0 | A | G | 20.9% | 594.6 / 117.5 | 239 | E1180E (GAA→GAG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_bme_pgi | 1,950,292 | 0 | C | G | 20.4% | 404.8 / 106.4 | 178 | A77A (GCG→GCC) | aspS | aspartyl‑tRNA synthetase |
| * | NC_000913_3_bme_pgi | 4,312,081 | 0 | G | C | 20.4% | 545.0 / 130.2 | 225 | intergenic (‑38/+21) | alsB/alsR | D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR |
| * | NC_000913_3_bme_pgi | 1,950,306 | 0 | C | G | 20.1% | 419.1 / 106.4 | 181 | G73R (GGC→CGC) | aspS | aspartyl‑tRNA synthetase |
| Marginal new junction evidence (lowest skew 10 of 486 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_bme_pgi | = 1196374 | 235 (1.110) | 28 (0.170) +22 bp |
14/152 | 16.8 | 13.2% | intergenic (+1/+493) | icd/ymfD | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase/e14 prophage; putative SAM‑dependent methyltransferase |
| ? | NC_000913_3_bme_pgi | = 1211623 | 239 (1.120) | intergenic (+46/+57) | icdC/iraM | pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor | |||||
| * | ? | NC_000913_3_bme_pgi | = 225998 | NA (NA) | 44 (0.220) | 19/188 | 17.7 | NA | noncoding (240/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_bme_pgi | = 226015 | NA (NA) | noncoding (257/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_bme_pgi | 3946665 = | 220 (1.030) | 46 (0.230) | 17/184 | 18.4 | 19.0% | intergenic (+58/‑35) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_bme_pgi | 3946689 = | 185 (0.930) | intergenic (+82/‑11) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913_3_bme_pgi | = 385205 | 241 (1.130) | 36 (0.180) | 16/180 | 18.6 | 14.1% | intergenic (‑589/‑27) | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| ? | NC_000913_3_bme_pgi | = 385217 | 216 (1.110) | intergenic (‑601/‑15) | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_bme_pgi | = 227444 | NA (NA) | 56 (0.280) | 16/186 | 19.2 | NA | noncoding (1686/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_bme_pgi | = 227459 | NA (NA) | noncoding (1701/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_bme_pgi | 2728214 = | NA (NA) | 88 (0.430) | 16/188 | 19.4 | NA | noncoding (971/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_bme_pgi | 2728240 = | NA (NA) | noncoding (945/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_bme_pgi | = 2700568 | 259 (1.220) | 23 (0.130) | 11/158 | 19.4 | 10.0% | noncoding (49/77 nt) | ohsC | sRNA antisense regulator of shoB toxin |
| ? | NC_000913_3_bme_pgi | = 2700581 | 206 (1.200) | noncoding (62/77 nt) | ohsC | sRNA antisense regulator of shoB toxin | |||||
| * | ? | NC_000913_3_bme_pgi | = 3946688 | 198 (0.930) | 55 (0.280) | 15/184 | 19.6 | 22.9% | intergenic (+81/‑12) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_bme_pgi | = 4171601 | NA (NA) | intergenic (+57/‑36) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon | |||||
| * | ? | NC_000913_3_bme_pgi | 3083831 = | 235 (1.110) | 31 (0.160) | 14/178 | 19.6 | 12.9% | intergenic (‑34/+104) | speB/speA | agmatinase/biosynthetic arginine decarboxylase, PLP‑binding |
| ? | NC_000913_3_bme_pgi | 3083868 = | 207 (1.070) | intergenic (‑71/+67) | speB/speA | agmatinase/biosynthetic arginine decarboxylase, PLP‑binding | |||||
| * | ? | NC_000913_3_bme_pgi | 1886815 = | 218 (1.030) | 31 (0.160) | 13/174 | 19.8 | 13.4% | intergenic (+5/+49) | yeaX/rnd | putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D |
| ? | NC_000913_3_bme_pgi | 1886858 = | 206 (1.090) | intergenic (+48/+6) | yeaX/rnd | putative YeaWX dioxygenase beta subunit, reductase component/ribonuclease D | |||||