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 (highest frequency 20 of 25 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_bme_pgi | 1,018,983 | 0 | A | T | 28.0% | 84.6 / 43.5 | 51 | intergenic (+46/+30) | matP/ompA | Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d) |
| * | NC_000913_3_bme_pgi | 4,296,061 | 0 | C | T | 27.5% | 112.0 / 48.7 | 69 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_bme_pgi | 1,018,986 | 0 | A | T | 27.5% | 83.9 / 42.6 | 51 | intergenic (+49/+27) | matP/ompA | Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d) |
| * | NC_000913_3_bme_pgi | 83,590 | 0 | G | T | 26.5% | 139.9 / 44.7 | 68 | intergenic (‑61/+32) | leuA/leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| * | NC_000913_3_bme_pgi | 3,439,588 | 0 | G | C | 25.0% | 104.9 / 38.2 | 52 | intergenic (‑79/+28) | yhdN/rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| * | NC_000913_3_bme_pgi | 83,587 | 0 | A | C | 24.3% | 120.2 / 48.5 | 70 | intergenic (‑58/+35) | leuA/leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| * | NC_000913_3_bme_pgi | 3,439,589 | 0 | G | C | 23.6% | 114.5 / 39.4 | 55 | intergenic (‑80/+27) | yhdN/rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| * | NC_000913_3_bme_pgi | 2,637,433 | 0 | C | T | 22.8% | 106.1 / 28.5 | 57 | intergenic (‑77/+41) | der/bamB | GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein |
| * | NC_000913_3_bme_pgi | 1,788,336 | 0 | A | T | 22.6% | 65.9 / 13.8 | 31 | intergenic (+58/‑99) | ppsR/aroH | PEP synthase kinase and PEP synthase pyrophosphorylase/3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible |
| * | NC_000913_3_bme_pgi | 2,637,439 | 0 | C | A | 21.1% | 134.3 / 24.8 | 52 | intergenic (‑83/+35) | der/bamB | GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein |
| * | NC_000913_3_bme_pgi | 3,156,590 | 0 | C | A | 21.1% | 127.6 / 25.9 | 52 | intergenic (+72/‑33) | yqhD/dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| * | NC_000913_3_bme_pgi | 1,757,688 | 0 | T | A | 21.1% | 80.1 / 21.6 | 38 | intergenic (+31/+33) | lpp/ldtE | murein lipoprotein/murein L,D‑transpeptidase |
| * | NC_000913_3_bme_pgi | 4,426,593 | 0 | T | A | 21.1% | 84.9 / 21.1 | 38 | intergenic (+35/+36) | rplI/yjfZ | 50S ribosomal subunit protein L9/uncharacterized protein |
| * | NC_000913_3_bme_pgi | 3,183,345 | 1 | . | T | 20.9% | 115.4 / 39.1 | 43 | intergenic (+22/+468) | zupT/ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| * | NC_000913_3_bme_pgi | 3,183,350 | 0 | A | . | 20.9% | 123.6 / 30.6 | 43 | intergenic (+27/+463) | zupT/ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| * | NC_000913_3_bme_pgi | 2,637,438 | 0 | T | G | 20.8% | 113.5 / 31.5 | 53 | intergenic (‑82/+36) | der/bamB | GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein |
| * | NC_000913_3_bme_pgi | 553,885 | 0 | G | A | 20.7% | 55.0 / 11.3 | 29 | T19I (ACC→ATC) | lpxH | UDP‑2,3‑diacylglucosamine pyrophosphohydrolase |
| * | NC_000913_3_bme_pgi | 553,887 | 0 | G | C | 20.7% | 67.0 / 15.1 | 29 | I18M (ATC→ATG) ‡ | lpxH | UDP‑2,3‑diacylglucosamine pyrophosphohydrolase |
| * | NC_000913_3_bme_pgi | 553,889 | 0 | T | C | 20.7% | 55.6 / 10.6 | 29 | I18V (ATC→GTC) ‡ | lpxH | UDP‑2,3‑diacylglucosamine pyrophosphohydrolase |
| * | NC_000913_3_bme_pgi | 2,637,444 | 0 | A | G | 20.4% | 110.0 / 23.3 | 54 | intergenic (‑88/+30) | der/bamB | GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 380 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_bme_pgi | 1097275 = | 13 (0.270) | 14 (0.310) | 13/238 | 3.2 | 54.7% | intergenic (+446/+290) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_bme_pgi | 1097295 = | 11 (0.240) | intergenic (+466/+270) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913_3_bme_pgi | 662673 = | 31 (0.640) | 13 (0.290) | 12/234 | 3.4 | 28.7% | intergenic (‑31/+79) | ybeD/dacA | UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5) |
| ? | NC_000913_3_bme_pgi | 662697 = | 36 (0.810) | intergenic (‑55/+55) | ybeD/dacA | UPF0250 family protein/D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5) | |||||
| * | ? | NC_000913_3_bme_pgi | 1097287 = | 12 (0.250) | 13 (0.290) | 12/238 | 3.5 | 52.8% | intergenic (+458/+278) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_bme_pgi | 1097464 = | 12 (0.260) | intergenic (+635/+101) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913_3_bme_pgi | 1613266 = | 48 (0.990) | 13 (0.270) | 12/254 | 3.8 | 22.6% | intergenic (‑15/+49) | glsB/sad | glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| ? | NC_000913_3_bme_pgi | 1613290 = | 41 (0.850) | intergenic (‑39/+25) | glsB/sad | glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent | |||||
| * | ? | NC_000913_3_bme_pgi | = 1028374 | NA (NA) | 10 (0.230) | 10/226 | 3.8 | NA | noncoding (9/24 nt) | REP88 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP88 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913_3_bme_pgi | = 1028380 | NA (NA) | noncoding (15/24 nt) | REP88 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP88 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | 1097172 = | NA (NA) | 11 (0.230) | 11/248 | 3.9 | 31.1% | intergenic (+343/+393) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_bme_pgi | 1097188 = | 25 (0.520) | intergenic (+359/+377) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913_3_bme_pgi | 225154 = | NA (NA) | 13 (0.280) | 11/244 | 3.9 | NA | noncoding (1384/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_bme_pgi | 225176 = | NA (NA) | noncoding (1406/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_bme_pgi | 3423376 = | 38 (0.790) | 16 (0.340) | 11/250 | 4.0 | 27.3% | intergenic (+182/+47) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| ? | NC_000913_3_bme_pgi | = 4213162 | 48 (1.010) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||
| * | ? | NC_000913_3_bme_pgi | = 446785 | 33 (0.680) | 10 (0.220) | 10/234 | 4.0 | 24.6% | intergenic (‑119/+30) | yajR/cyoE | putative transporter/protoheme IX farnesyltransferase |
| ? | NC_000913_3_bme_pgi | = 446789 | 31 (0.700) | intergenic (‑123/+26) | yajR/cyoE | putative transporter/protoheme IX farnesyltransferase | |||||
| * | ? | NC_000913_3_bme_pgi | 1436221 = | 64 (1.320) | 10 (0.220) | 10/238 | 4.1 | 15.4% | coding (673/1134 nt) | ompN | outer membrane pore protein N, non‑specific |
| ? | NC_000913_3_bme_pgi | 1436253 = | 50 (1.100) | coding (641/1134 nt) | ompN | outer membrane pore protein N, non‑specific | |||||