mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 87 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,741,273 | 1 | . | C | 71.2% | 161.3 / 65.4 | 66 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,275 | 0 | A | G | 71.2% | 90.1 / 44.4 | 66 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 59.7% | 20.3 / 190.2 | 176 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,725 | 0 | A | G | 59.3% | 57.1 / 111.9 | 108 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 57.6% | 43.9 / 150.5 | 140 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,070,268 | 0 | G | C | 56.1% | 0.7 / 79.1 | 57 | intergenic (+65/+79) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947 | 4,741,301 | 0 | A | C | 51.9% | 1.1 / 111.0 | 79 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 51.9% | 12.2 / 131.8 | 79 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,070,265 | 0 | G | C | 51.7% | ‑4.3 / 86.0 | 58 | intergenic (+62/+82) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947 | 4,741,299 | 0 | C | T | 51.3% | ‑2.4 / 108.4 | 79 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | C | 51.3% | 124.7 / 157.7 | 79 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 49.4% | 1.2 / 110.0 | 79 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 195,634 | 0 | C | T | 48.3% | 35.0 / 231.9 | 176 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,741,298 | 1 | . | T | 48.1% | 134.2 / 185.4 | 79 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 5,655,687 | 0 | C | A | 46.2% | 54.2 / 115.8 | 91 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 1,403,596 | 0 | G | A | 45.6% | 14.8 / 65.1 | 57 | intergenic (‑56/+25) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947 | 1,403,597 | 0 | T | C | 45.6% | 12.3 / 67.1 | 57 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947 | 5,655,692 | 0 | T | . | 44.7% | 149.7 / 148.0 | 85 | intergenic (‑96/+56) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 5,655,682 | 0 | T | G | 44.1% | 37.7 / 130.0 | 93 | intergenic (‑86/+66) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 1,506,936 | 0 | G | A | 43.9% | 13.9 / 46.4 | 41 | intergenic (+48/‑69) | petC/sspA | ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A |
| Marginal new junction evidence (lowest skew 10 of 1083 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 337784 = | 86 (0.780) | 39 (0.450) | 26/208 | 3.4 | 39.1% | intergenic (‑31/+98) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| ? | NC_002947 | 337868 = | 54 (0.620) | intergenic (‑115/+14) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease | |||||
| * | ? | NC_002947 | 1967188 = | 67 (0.610) | 26 (0.320) | 22/198 | 3.9 | 34.9% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967284 = | 47 (0.570) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 4896443 | 60 (0.540) | 41 (0.440) | 23/222 | 4.4 | 46.2% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4896490 | 45 (0.490) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 2553944 | NA (NA) | 86 (0.850) | 25/242 | 4.5 | 57.3% | intergenic (+32/‑119) | PP_5SF/PP_2240 | 5S ribosomal RNA/ABC transporter permease/ATP‑binding protein |
| ? | NC_002947 | 5307467 = | 70 (0.630) | intergenic (‑168/+18) | recC/PP_5SG | multifunctional ATP‑dependent DNA helicase/dsDNA/ssDNA exonuclease/ssDNA endonuclease recombinase subunit/5S ribosomal RNA | |||||
| * | ? | NC_002947 | 5201627 = | 83 (0.750) | 28 (0.350) | 18/190 | 4.6 | 36.2% | intergenic (‑65/‑115) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | 5201722 = | 39 (0.490) | intergenic (‑160/‑20) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | 6009165 = | 63 (0.570) | 29 (0.350) | 18/198 | 4.8 | 44.2% | intergenic (+6/+76) | norM/PP_5263 | multidrug resistance protein NorM/GGDEF domain‑containing protein |
| ? | NC_002947 | 6009242 = | 26 (0.320) | coding (1667/1668 nt) | PP_5263 | GGDEF domain‑containing protein | |||||
| * | ? | NC_002947 | 6006595 = | 59 (0.530) | 25 (0.310) | 17/192 | 4.9 | 36.0% | intergenic (+7/+92) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947 | 6006679 = | 46 (0.570) | intergenic (+91/+8) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | 5477138 = | 100 (0.910) | 30 (0.400) | 15/182 | 5.1 | 36.4% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5477237 = | 36 (0.470) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | = 4586100 | 89 (0.810) | 27 (0.340) | 16/188 | 5.1 | 33.9% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 42 (0.540) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4861197 | 98 (0.890) | 30 (0.340) | 18/214 | 5.3 | 28.5% | intergenic (‑103/+134) | ligA/PP_4275 | DNA ligase/cell division protein ZipA |
| ? | NC_002947 | = 4861238 | 71 (0.800) | intergenic (‑144/+93) | ligA/PP_4275 | DNA ligase/cell division protein ZipA | |||||