mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
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 | 3,781,152 | 0 | A | G | 35.3% | 23.5 / 18.7 | 35 | intergenic (+135/‑63) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 155,349 | 0 | A | C | 34.7% | 45.7 / 54.6 | 49 | T26T (ACT→ACG) | htrE | putative outer membrane usher protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.7% | 150.7 / 53.5 | 87 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 2,676,186 | 0 | A | G | 23.5% | 88.7 / 26.5 | 51 | L214L (TTG→CTG) | yphD | putative sugar ABC transporter permease |
| * | NC_000913 | 3,972,647 | 0 | G | A | 23.5% | 117.3 / 35.3 | 68 | M42I (ATG→ATA) | rffG | dTDP‑glucose 4,6‑dehydratase |
| * | NC_000913 | 1,895,122 | 0 | A | T | 22.9% | 124.3 / 36.0 | 61 | A106A (GCA→GCT) | pabB | aminodeoxychorismate synthase, subunit I |
| * | NC_000913 | 560,243 | 0 | A | G | 22.4% | 108.1 / 27.9 | 58 | N183D (AAT→GAT) | sfmD | putative outer membrane export usher protein |
| * | NC_000913 | 2,057,862 | 0 | T | C | 22.2% | 74.3 / 22.7 | 45 | intergenic (+288/+165) | yeeN/asnW | UPF0082 family protein/tRNA‑Asn |
| * | NC_000913 | 145,758 | 0 | G | T | 22.0% | 117.8 / 27.9 | 50 | K226N (AAG→AAT) | yadE | putative polysaccharide deacetylase lipoprotein |
| * | NC_000913 | 1,235,039 | 0 | A | G | 22.0% | 94.2 / 24.7 | 50 | E34E (GAA→GAG) | fadR | fatty acid metabolism regulon transcriptional regulator |
| * | NC_000913 | 2,774,626 | 0 | A | . | 21.5% | 187.2 / 47.0 | 65 | coding (1309/1704 nt) | yfjW | CP4‑57 prophage; putative inner membrane protein |
| * | NC_000913 | 3,298,363 | 0 | G | A | 21.5% | 132.9 / 31.9 | 65 | L162F (CTT→TTT) | yraR | putative nucleoside‑diphosphate‑sugar epimerase |
| * | NC_000913 | 2,553,031 | 0 | C | T | 21.3% | 96.9 / 17.8 | 47 | A227V (GCA→GTA) | amiA | N‑acetylmuramoyl‑l‑alanine amidase I |
| * | NC_000913 | 3,479,751 | 1 | . | C | 21.1% | 131.9 / 49.0 | 52 | coding (857/1806 nt) | kefB | potassium:proton antiporter |
| * | NC_000913 | 543,210 | 0 | A | T | 20.4% | 103.5 / 20.8 | 44 | intergenic (+177/+51) | glxK/allE | glycerate kinase II/S‑ureidoglycine aminohydrolase |
| * | NC_000913 | 2,037,333 | 0 | T | . | 20.4% | 136.6 / 31.8 | 49 | coding (820/1359 nt) | yedV | putative sensory kinase in two‑component regulatory system with YedW |
| * | NC_000913 | 2,580,172 | 0 | T | C | 20.4% | 92.9 / 17.8 | 50 | G179G (GGT→GGC) | tktB | transketolase 2, thiamine triphosphate‑binding |
| * | NC_000913 | 2,888,383 | 0 | A | G | 20.4% | 106.8 / 24.4 | 56 | intergenic (‑71/+4) | cysH/cysI | phosphoadenosine phosphosulfate reductase; PAPS reductase, thioredoxin dependent/sulfite reductase, beta subunit, NAD(P)‑binding, heme‑binding |
| * | NC_000913 | 543,207 | 0 | A | T | 20.0% | 107.3 / 20.1 | 45 | intergenic (+174/+54) | glxK/allE | glycerate kinase II/S‑ureidoglycine aminohydrolase |
| Marginal new junction evidence (lowest skew 10 of 273 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 225281 | NA (NA) | 14 (0.280) | 12/188 | 4.5 | NA | noncoding (1511/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 225293 | NA (NA) | noncoding (1523/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 275007 | NA (NA) | 10 (0.190) | 8/192 | 6.1 | NA | noncoding (143/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 275025 | NA (NA) | noncoding (125/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1691580 | 65 (1.210) | 5 (0.130) +30 bp |
4/138 | 6.2 | 10.0% | intergenic (+220/+6) | ydgA/uidC | DUF945 family protein/putative outer membrane porin for beta‑glucuronides porin protein |
| ? | NC_000913 | 2001967 = | NA (NA) | intergenic (‑178/+143) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin) | |||||
| * | ? | NC_000913 | = 216089 | NA (NA) | 5 (0.130) +30 bp |
4/138 | 6.2 | 10.0% | noncoding (63/111 nt) | RIP16 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP16 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 1691580 | 65 (1.210) | intergenic (+220/+6) | ydgA/uidC | DUF945 family protein/putative outer membrane porin for beta‑glucuronides porin protein | |||||
| * | ? | NC_000913 | = 4171607 | 12 (0.220) | 24 (0.480) | 7/186 | 6.4 | 68.1% | intergenic (+63/‑30) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| ? | NC_000913 | = 4213022 | NA (NA) | intergenic (+76/‑18) | rrlE/rrfE | 23S ribosomal RNA of rrnE operon/5S ribosomal RNA of rrnE operon | |||||
| * | ? | NC_000913 | = 3946688 | 58 (1.080) | 24 (0.480) | 7/186 | 6.4 | 30.6% | intergenic (+81/‑12) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4171601 | NA (NA) | intergenic (+57/‑36) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon | |||||
| * | ? | NC_000913 | 2726200 = | NA (NA) | 24 (0.480) | 7/186 | 6.4 | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | = 228744 | 23 (0.430) | 24 (0.480) | 7/186 | 6.4 | 52.6% | intergenic (+82/‑12) | rrlH/rrfH | 23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | = 3060667 | NA (NA) | 6 (0.120) | 6/182 | 6.7 | NA | noncoding (8/21 nt) | REP212 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP212 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | = 3060672 | NA (NA) | noncoding (13/21 nt) | REP212 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP212 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | 3056789 = | 52 (0.970) | 6 (0.120) | 6/182 | 6.7 | 10.6% | coding (549/549 nt) | fau | 5‑formyltetrahydrofolate cyclo‑ligase family protein |
| ? | NC_000913 | 3056813 = | 53 (1.080) | intergenic (+24/+77) | fau/ibsC | 5‑formyltetrahydrofolate cyclo‑ligase family protein/toxic membrane protein | |||||