mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.2 revision caddc01d3be9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 80 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,127 | 0 | C | T | 64.8% | 31.2 / 79.7 | 88 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,741,273 | 1 | . | C | 64.1% | 83.6 / 49.4 | 39 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,275 | 0 | A | G | 64.1% | 35.3 / 30.2 | 39 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | C | 54.5% | 70.9 / 81.8 | 45 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 53.3% | ‑5.0 / 70.9 | 45 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 699,725 | 0 | A | G | 53.0% | 1.7 / 82.8 | 66 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 52.3% | ‑5.6 / 138.7 | 108 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,741,299 | 0 | C | T | 52.3% | ‑2.6 / 58.0 | 45 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 51.1% | ‑0.9 / 56.8 | 45 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 195,634 | 0 | C | T | 49.6% | 24.0 / 150.2 | 115 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,741,298 | 1 | . | T | 46.7% | 71.6 / 102.0 | 45 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 46.7% | ‑4.4 / 54.1 | 45 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,578,321 | 0 | T | G | 45.0% | ‑0.4 / 86.3 | 60 | T1040P (ACC→CCC) | ttgB | efflux pump membrane protein TtgB |
| * | NC_002947 | 2,282,813 | 0 | T | G | 41.3% | 21.2 / 52.2 | 46 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,506,932 | 0 | A | G | 38.5% | 18.7 / 22.9 | 26 | intergenic (+44/‑73) | petC/sspA | ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A |
| * | NC_002947 | 5,988,961 | 0 | T | C | 37.8% | 104.4 / 88.0 | 90 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 1,070,268 | 0 | G | C | 37.0% | 24.5 / 23.9 | 27 | intergenic (+65/+79) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947 | 4,741,274 | 0 | A | C | 35.9% | 35.1 / 29.3 | 39 | intergenic (+465/+287) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,184,591 | 0 | G | C | 34.6% | 34.6 / 20.6 | 26 | intergenic (‑201/‑211) | mltF/purL | membrane‑bound lytic murein transglycosylase F/phosphoribosylformylglycinamidine synthase |
| * | NC_002947 | 1,184,594 | 0 | G | C | 34.6% | 32.7 / 22.6 | 26 | intergenic (‑204/‑208) | mltF/purL | membrane‑bound lytic murein transglycosylase F/phosphoribosylformylglycinamidine synthase |
| Marginal new junction evidence (lowest skew 10 of 267 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 1544501 = | 38 (0.520) | 18 (0.320) | 13/210 | 4.1 | 45.9% | intergenic (+18/+96) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| ? | NC_002947 | 1544577 = | 13 (0.230) | intergenic (+94/+20) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG | |||||
| * | ? | NC_002947 | = 5914240 | 42 (0.580) | 12 (0.210) | 11/214 | 4.8 | 29.9% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | = 5914280 | 23 (0.400) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | = 1419584 | 29 (0.400) | 11 (0.200) | 10/206 | 4.9 | 32.8% | intergenic (‑67/+70) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1419614 | 23 (0.410) | intergenic (‑97/+40) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 4586100 | 45 (0.620) | 12 (0.230) | 9/194 | 5.0 | 31.1% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 21 (0.400) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4896443 | 28 (0.380) | 12 (0.200) | 11/228 | 5.1 | 29.8% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4896490 | 33 (0.540) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 1780127 | 24 (0.330) | 12 (0.190) | 11/232 | 5.2 | 33.5% | intergenic (+44/+62) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | = 1780151 | 27 (0.430) | intergenic (+68/+38) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | 4340085 = | 30 (0.410) | 12 (0.220) | 8/202 | 5.6 | 39.1% | intergenic (+26/‑305) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| ? | NC_002947 | 4340169 = | 15 (0.280) | intergenic (+110/‑221) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein | |||||
| * | ? | NC_002947 | 4896423 = | 31 (0.430) | 9 (0.150) | 9/228 | 5.8 | 23.9% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896512 = | 31 (0.500) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 1126618 | 61 (0.840) | 14 (0.230) | 9/228 | 5.8 | 23.6% | intergenic (‑67/+83) | tdcG‑II/gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| ? | NC_002947 | = 1126634 | 39 (0.630) | intergenic (‑83/+67) | tdcG‑II/gcvP‑I | L‑serine dehydratase/glycine dehydrogenase | |||||
| * | ? | NC_002947 | = 1970782 | 44 (0.600) | 9 (0.150) | 9/230 | 5.9 | 19.9% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1970844 | 35 (0.560) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||