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 83 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 | 73.4% | 161.7 / 61.5 | 64 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,275 | 0 | A | G | 73.4% | 101.4 / 39.1 | 64 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,298 | 1 | . | T | 67.1% | 163.2 / 78.0 | 70 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 67.1% | 87.2 / 50.8 | 70 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 67.1% | 96.2 / 104.5 | 70 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,403,596 | 0 | G | A | 61.0% | 23.6 / 39.8 | 41 | intergenic (‑56/+25) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947 | 1,403,597 | 0 | T | C | 61.0% | 21.3 / 38.3 | 41 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947 | 1,327,127 | 0 | C | T | 58.8% | 6.8 / 214.6 | 188 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,725 | 0 | A | G | 58.3% | 52.8 / 115.9 | 108 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 48.5% | 19.0 / 226.1 | 167 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 43,457 | 0 | T | . | 48.1% | 44.3 / 47.9 | 27 | intergenic (+23/+70) | PP_0040/cadA‑I | hypothetical protein/cadmium translocating P‑type ATPase |
| * | NC_002947 | 195,634 | 0 | C | T | 43.6% | 100.7 / 208.3 | 180 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 43,461 | 1 | . | A | 43.3% | 8.1 / 58.7 | 30 | intergenic (+27/+66) | PP_0040/cadA‑I | hypothetical protein/cadmium translocating P‑type ATPase |
| * | NC_002947 | 5,655,682 | 0 | T | G | 40.0% | 34.4 / 76.0 | 60 | intergenic (‑86/+66) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 4,842,941 | 0 | C | . | 39.0% | 116.2 / 92.6 | 59 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 1,544,536 | 0 | C | G | 38.5% | 33.0 / 27.4 | 26 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,541 | 0 | C | G | 38.5% | 33.0 / 27.3 | 26 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,543 | 0 | G | C | 38.5% | 30.2 / 27.9 | 26 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 2,951,377 | 0 | G | C | 37.5% | 52.9 / 67.6 | 56 | intergenic (‑113/+48) | oguA/PP_2585 | 8‑oxoguanine deaminase/alpha‑ketoglutaric semialdehyde dehydrogenase |
| * | NC_002947 | 4,049,954 | 0 | C | G | 37.5% | 56.0 / 69.3 | 56 | intergenic (+43/‑58) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| Marginal new junction evidence (lowest skew 10 of 658 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808219 = | 0 (0.000) | 35 (0.410) | 26/194 | 3.3 | 51.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 67 (0.790) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5537105 | 76 (0.650) | 28 (0.300) | 19/210 | 5.2 | 34.5% | intergenic (+34/+69) | nadE/PP_4870 | NH(3)‑dependent NAD(+) synthetase/azurin |
| ? | NC_002947 | = 5537127 | 46 (0.500) | intergenic (+56/+47) | nadE/PP_4870 | NH(3)‑dependent NAD(+) synthetase/azurin | |||||
| * | ? | NC_002947 | 6009165 = | 46 (0.400) | 25 (0.290) | 17/198 | 5.4 | 41.9% | intergenic (+6/+76) | norM/PP_5263 | multidrug resistance protein NorM/GGDEF domain‑containing protein |
| ? | NC_002947 | 6009242 = | 35 (0.400) | coding (1667/1668 nt) | PP_5263 | GGDEF domain‑containing protein | |||||
| * | ? | NC_002947 | 353061 = | 40 (0.340) | 23 (0.250) | 16/206 | 5.9 | 44.2% | intergenic (+25/+93) | hisF/cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein |
| ? | NC_002947 | 353133 = | 27 (0.300) | intergenic (+97/+21) | hisF/cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein | |||||
| * | ? | NC_002947 | 5914213 = | 47 (0.400) | 20 (0.220) | 16/208 | 6.0 | 33.1% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | 5914309 = | 44 (0.480) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | = 6006630 | 52 (0.450) | 20 (0.240) | 14/192 | 6.1 | 36.8% | intergenic (+42/+57) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947 | = 6006642 | 31 (0.370) | intergenic (+54/+45) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | 5477138 = | 80 (0.690) | 16 (0.200) | 13/182 | 6.1 | 24.4% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5477237 = | 44 (0.550) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | = 4586100 | 66 (0.570) | 13 (0.160) | 13/188 | 6.3 | 24.3% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 34 (0.410) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 5816910 = | 63 (0.540) | 26 (0.260) | 16/228 | 6.6 | 38.1% | intergenic (+40/+89) | PP_5092/pilT | NLP/P60 protein/twitching motility protein |
| ? | NC_002947 | 5816973 = | 30 (0.300) | intergenic (+103/+26) | PP_5092/pilT | NLP/P60 protein/twitching motility protein | |||||
| * | ? | NC_002947 | 337784 = | 77 (0.660) | 19 (0.210) | 14/208 | 6.6 | 24.8% | intergenic (‑31/+98) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| ? | NC_002947 | 337868 = | 55 (0.600) | intergenic (‑115/+14) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease | |||||