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 46 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 63.2% | 23.9 / 93.4 | 95 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,722 | 0 | A | G | 56.3% | 19.2 / 79.9 | 71 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,340,089 | 0 | G | C | 50.0% | ‑3.5 / 14.6 | 12 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,090 | 0 | A | T | 50.0% | ‑6.7 / 13.5 | 12 | intergenic (+75/‑256) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,081 | 0 | A | G | 46.2% | ‑1.2 / 13.0 | 13 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,082 | 0 | C | T | 46.2% | ‑0.0 / 11.4 | 13 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 196,879 | 0 | G | A | 44.0% | 13.0 / 25.3 | 25 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 195,634 | 0 | C | T | 43.3% | 64.3 / 118.0 | 104 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,075 | 0 | A | T | 40.0% | 7.1 / 10.2 | 15 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,076 | 0 | G | C | 40.0% | 10.1 / 13.8 | 15 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,348,705 | 0 | A | G | 38.4% | 90.1 / 99.0 | 100 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 2,282,770 | 0 | T | G | 34.6% | 33.3 / 52.1 | 52 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 195,559 | 0 | C | A | 33.3% | 100.7 / 63.0 | 69 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,282,779 | 0 | C | A | 32.6% | 42.2 / 31.8 | 47 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,774 | 0 | G | C | 31.9% | 43.9 / 39.5 | 48 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,775 | 0 | G | C | 31.9% | 45.4 / 41.2 | 48 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 196,351 | 0 | C | G | 30.4% | 132.3 / 68.8 | 92 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,740,839 | 0 | C | G | 28.8% | 75.5 / 36.1 | 52 | intergenic (+76/+677) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,740,841 | 0 | T | A | 28.8% | 66.4 / 31.3 | 52 | intergenic (+78/+675) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 441,326 | 0 | G | . | 28.1% | 73.4 / 28.0 | 32 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| Marginal new junction evidence (lowest skew 10 of 321 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 5594092 = | 41 (0.600) | 10 (0.180) | 9/228 | 5.6 | 22.0% | intergenic (‑39/+106) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase |
| ? | NC_002947 | 5594185 = | 38 (0.700) | intergenic (‑132/+13) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||
| * | ? | NC_002947 | 4647557 = | 29 (0.430) | 8 (0.160) | 7/206 | 5.9 | 26.2% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647665 = | 24 (0.490) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | 2301496 = | 28 (0.410) | 10 (0.160) | 10/256 | 5.9 | 17.2% | intergenic (‑140/‑191) | sbcD/PP_5497 | exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein |
| ? | NC_002947 | 2301581 = | 71 (1.160) | intergenic (‑225/‑106) | sbcD/PP_5497 | exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein | |||||
| * | ? | NC_002947 | = 5594119 | 47 (0.690) | 8 (0.150) | 8/228 | 6.0 | 17.4% | intergenic (‑66/+79) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase |
| ? | NC_002947 | = 5594156 | 38 (0.700) | intergenic (‑103/+42) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||
| * | ? | NC_002947 | 1487006 = | 63 (0.930) | 8 (0.150) | 7/224 | 6.4 | 14.9% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947 | 1487096 = | 42 (0.780) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947 | 4808174 = | 3 (0.040) | 9 (0.180) | 6/214 | 6.6 | 33.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988935 | 34 (0.660) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 478290 | 41 (0.600) | 7 (0.130) | 6/224 | 6.9 | 20.5% | intergenic (+38/+72) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase |
| ? | NC_002947 | = 478325 | 22 (0.410) | intergenic (+73/+37) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase | |||||
| * | ? | NC_002947 | 6098849 = | 64 (0.940) | 8 (0.130) | 7/266 | 7.4 | 12.5% | coding (240/867 nt) | PP_5350 | RpiR family transcriptional regulator |
| ? | NC_002947 | 6098886 = | 52 (0.820) | coding (203/867 nt) | PP_5350 | RpiR family transcriptional regulator | |||||
| * | ? | NC_002947 | = 5477130 | 27 (0.400) | 4 (0.080) | 4/202 | 7.4 | 18.1% | intergenic (+43/+69) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | = 5477147 | 17 (0.350) | intergenic (+60/+52) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | 1602056 = | 75 (1.100) | 7 (0.120) +TGCACCGCAGTGCTTGC |
6/250 | 7.5 | 11.5% | intergenic (+69/‑98) | PP_1404/PP_5469 | hypothetical protein/SAM‑dependent methyltransferase |
| ? | NC_002947 | = 5594119 | 47 (0.690) | intergenic (‑66/+79) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||