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 130 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,637,367 | 0 | A | T | 55.6% | ‑4.6 / 20.1 | 18 | intergenic (+34/+32) | pdxJ/PP_1437 | pyridoxine 5'‑phosphate synthase/heavy metal sensor histidine kinase |
| * | NC_002947 | 1,637,368 | 0 | A | T | 55.6% | ‑4.5 / 19.9 | 18 | intergenic (+35/+31) | pdxJ/PP_1437 | pyridoxine 5'‑phosphate synthase/heavy metal sensor histidine kinase |
| * | NC_002947 | 4,107,598 | 0 | T | A | 54.5% | ‑2.9 / 10.3 | 11 | intergenic (+38/+47) | PP_3612/PP_3613 | TonB‑dependent receptor/L‑sorbosone dehydrogenase |
| * | NC_002947 | 4,107,599 | 0 | C | G | 54.5% | ‑2.8 / 11.2 | 11 | intergenic (+39/+46) | PP_3612/PP_3613 | TonB‑dependent receptor/L‑sorbosone dehydrogenase |
| * | NC_002947 | 4,107,600 | 0 | T | A | 54.5% | ‑3.7 / 10.3 | 11 | intergenic (+40/+45) | PP_3612/PP_3613 | TonB‑dependent receptor/L‑sorbosone dehydrogenase |
| * | NC_002947 | 3,056,698 | 0 | A | C | 47.1% | ‑3.3 / 13.7 | 17 | intergenic (‑208/+100) | PP_2666/PP_2667 | hypothetical protein/ABC transporter permease |
| * | NC_002947 | 1,637,357 | 0 | T | C | 46.7% | ‑1.4 / 13.7 | 15 | intergenic (+24/+42) | pdxJ/PP_1437 | pyridoxine 5'‑phosphate synthase/heavy metal sensor histidine kinase |
| * | NC_002947 | 284,588 | 0 | T | A | 46.2% | ‑1.4 / 10.3 | 14 | intergenic (+34/+29) | betT‑II/atsK | choline/carnitine/betaine transporter/alpha‑ketoglutarate‑dependent sulfonate dioxygenase |
| * | NC_002947 | 699,725 | 0 | A | G | 46.2% | 4.7 / 28.4 | 26 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,350,671 | 0 | A | G | 45.7% | 10.0 / 41.5 | 35 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 45.2% | 13.4 / 36.3 | 31 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 5,990,802 | 0 | C | T | 43.8% | 10.0 / 14.7 | 16 | intergenic (+118/‑428) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,990,803 | 0 | G | T | 43.8% | 12.6 / 17.4 | 16 | intergenic (+119/‑427) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,990,804 | 0 | C | T | 43.8% | 9.0 / 14.7 | 16 | intergenic (+120/‑426) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,990,807 | 0 | A | G | 43.8% | 10.6 / 14.8 | 16 | intergenic (+123/‑423) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,990,815 | 0 | C | G | 43.8% | 13.8 / 15.9 | 16 | intergenic (+131/‑415) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,990,818 | 0 | C | T | 43.8% | 9.1 / 13.5 | 16 | intergenic (+134/‑412) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 284,587 | 0 | T | A | 42.9% | ‑1.6 / 10.3 | 14 | intergenic (+33/+30) | betT‑II/atsK | choline/carnitine/betaine transporter/alpha‑ketoglutarate‑dependent sulfonate dioxygenase |
| * | NC_002947 | 4,844,863 | 0 | C | . | 42.9% | 19.5 / 19.7 | 14 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 4,947,199 | 0 | A | G | 42.9% | 4.1 / 20.8 | 21 | intergenic (+592/+206) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein |
| Marginal new junction evidence (lowest skew 10 of 52 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 2564260 = | 31 (1.860) | 4 (0.250) | 4/272 | 1.5 | 12.6% | coding (33/1137 nt) | dauA | FAD‑dependent catabolic D‑arginine dehydrogenase |
| ? | NC_002947 | 2564308 = | 26 (1.640) | coding (81/1137 nt) | dauA | FAD‑dependent catabolic D‑arginine dehydrogenase | |||||
| * | ? | NC_002947 | 4647267 = | 18 (1.080) | 4 (0.240) | 4/280 | 1.6 | 19.7% | coding (420/483 nt) | PP_5658 | hypothetical protein |
| ? | NC_002947 | 4647285 = | 15 (0.920) | coding (438/483 nt) | PP_5658 | hypothetical protein | |||||
| * | ? | NC_002947 | 3936797 = | 25 (1.500) | 4 (0.240) | 4/282 | 1.6 | 16.4% | coding (582/1911 nt) | PP_3467 | sigma‑54 dependent transcriptional regulator |
| ? | NC_002947 | 3936825 = | 16 (0.970) | coding (554/1911 nt) | PP_3467 | sigma‑54 dependent transcriptional regulator | |||||
| * | ? | NC_002947 | 1640954 = | 37 (2.220) | 4 (0.240) | 4/284 | 1.6 | 10.0% | coding (39/957 nt) | cmoB | tRNA 5‑methoxyuridine(34) synthase CmoB |
| ? | NC_002947 | 1640972 = | 35 (2.110) | coding (21/957 nt) | cmoB | tRNA 5‑methoxyuridine(34) synthase CmoB | |||||
| * | ? | NC_002947 | 1499443 = | 19 (1.140) | 3 (0.210) | 3/240 | 1.6 | 18.2% | intergenic (+13/‑153) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | 1499526 = | 11 (0.790) | intergenic (+96/‑70) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | 4751964 = | 17 (1.020) | 3 (0.200) | 3/252 | 1.7 | 19.4% | intergenic (+18/+54) | PP_4203/mqsA | ubiquinone oxidoreductase electron transfer flavoprotein/type II toxin‑antitoxin MqsRA system antitoxin/DNA‑binding transcriptional repressor |
| ? | NC_002947 | 4752008 = | 10 (0.680) | intergenic (+62/+10) | PP_4203/mqsA | ubiquinone oxidoreductase electron transfer flavoprotein/type II toxin‑antitoxin MqsRA system antitoxin/DNA‑binding transcriptional repressor | |||||
| * | ? | NC_002947 | 1138537 = | 16 (0.960) | 3 (0.200) | 3/258 | 1.7 | 19.1% | intergenic (‑62/+103) | arcC/arcB | carbamate kinase/ornithine carbamoyltransferase |
| ? | NC_002947 | 1138626 = | 11 (0.730) | intergenic (‑151/+14) | arcC/arcB | carbamate kinase/ornithine carbamoyltransferase | |||||
| * | ? | NC_002947 | 5866803 = | 17 (1.020) | 3 (0.190) | 3/272 | 1.8 | 14.6% | coding (1326/2253 nt) | cadA‑III | cadmium translocating P‑type ATPase |
| ? | NC_002947 | 5866845 = | 19 (1.200) | coding (1284/2253 nt) | cadA‑III | cadmium translocating P‑type ATPase | |||||
| * | ? | NC_002947 | 4775668 = | 14 (0.840) | 3 (0.190) | 3/276 | 1.8 | 18.5% | coding (5566/10413 nt) | pvdD | non‑ribosomal peptide synthetase |
| ? | NC_002947 | 4775685 = | 13 (0.810) | coding (5549/10413 nt) | pvdD | non‑ribosomal peptide synthetase | |||||
| * | ? | NC_002947 | 4747991 = | 23 (1.380) | 4 (0.250) | 3/276 | 1.8 | 15.9% | intergenic (‑18/+58) | PP_4200/etfA | hypothetical protein/electron transfer flavoprotein subunit alpha |
| ? | NC_002947 | 4748033 = | 20 (1.240) | intergenic (‑60/+16) | PP_4200/etfA | hypothetical protein/electron transfer flavoprotein subunit alpha | |||||