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 47 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 | 59.9% | 17.6 / 142.4 | 135 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 50.0% | 28.7 / 154.6 | 108 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,722 | 0 | A | G | 42.5% | 35.1 / 82.6 | 73 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 40.2% | 82.6 / 107.3 | 102 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,454,629 | 0 | C | A | 33.3% | 19.8 / 14.1 | 25 | R430S (CGC→AGC) | PP_4791 | transposase |
| * | NC_002947 | 3,853,118 | 0 | T | A | 30.8% | 28.1 / 13.7 | 26 | I169N (ATT→AAT) | alkB | alpha‑ketoglutarate‑ and Fe(II)‑dependent dioxygenase |
| * | NC_002947 | 5,454,627 | 0 | T | G | 29.2% | 23.8 / 17.4 | 24 | L429R (CTT→CGT) | PP_4791 | transposase |
| * | NC_002947 | 5,454,628 | 0 | T | A | 29.2% | 20.5 / 14.6 | 24 | L429L (CTT→CTA) | PP_4791 | transposase |
| * | NC_002947 | 4,583,571 | 0 | G | . | 27.3% | 50.1 / 17.0 | 22 | intergenic (‑144/+27) | treSB/glgE | bifunctional trehalose synthase B/maltokinase/alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase |
| * | NC_002947 | 5,988,905 | 0 | T | C | 27.2% | 135.1 / 60.7 | 93 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,740,467 | 0 | T | G | 26.9% | 78.1 / 40.3 | 67 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,988,911 | 0 | A | . | 26.4% | 227.9 / 87.1 | 93 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,740,470 | 0 | A | T | 26.2% | 99.5 / 35.5 | 67 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,740,471 | 0 | A | T | 26.2% | 100.9 / 37.3 | 67 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,988,894 | 0 | C | T | 24.7% | 162.9 / 53.9 | 93 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,895 | 0 | A | G | 24.7% | 157.4 / 53.0 | 93 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,049,910 | 0 | C | G | 24.7% | 121.5 / 43.5 | 73 | intergenic (+43/‑58) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| * | NC_002947 | 4,049,913 | 0 | C | T | 24.7% | 117.4 / 40.9 | 73 | intergenic (+46/‑55) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| * | NC_002947 | 5,740,474 | 0 | C | A | 24.6% | 138.9 / 35.2 | 69 | intergenic (+39/+32) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 4,049,907 | 0 | A | G | 24.4% | 128.5 / 44.3 | 79 | intergenic (+40/‑61) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| Marginal new junction evidence (lowest skew 10 of 586 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4808179 | 2 (0.030) | 33 (0.490) | 16/258 | 4.8 | 50.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 62 (0.930) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4074039 | NA (NA) | 24 (0.340) | 16/272 | 5.2 | NA | intergenic (‑577/+47) | mdtA/PP_3586 | multidrug transporter membrane fusion protein/transposase |
| ? | NC_002947 | = 4302647 | NA (NA) | intergenic (+1137/‑163) | PP_3774/PP_5627 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 5477130 | 56 (0.770) | 8 (0.150) | 8/200 | 6.0 | 15.3% | intergenic (+43/+69) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | = 5477147 | 49 (0.950) | intergenic (+60/+52) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | = 652782 | 57 (0.780) | 13 (0.210) | 11/242 | 6.0 | 34.3% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808159 | 1 (0.020) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 5477090 = | 69 (0.940) | 8 (0.150) | 7/200 | 6.5 | 14.1% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5477189 = | 49 (0.950) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | = 4586029 | 15 (0.210) | 15 (0.220) | 11/260 | 6.5 | 39.6% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586109 | 32 (0.480) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 174906 | NA (NA) | 14 (0.200) | 11/272 | 6.8 | NA | noncoding (1704/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | NC_002947 | = 174936 | NA (NA) | noncoding (1734/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | NC_002947 | = 1728634 | 63 (0.860) | 11 (0.150) | 11/276 | 6.9 | 14.8% | intergenic (+28/+95) | cspA‑I/PP_1523 | major cold shock protein/hypothetical protein |
| ? | NC_002947 | = 1728695 | 65 (0.910) | intergenic (+89/+34) | cspA‑I/PP_1523 | major cold shock protein/hypothetical protein | |||||
| * | ? | NC_002947 | 1487006 = | 58 (0.790) | 7 (0.120) | 7/222 | 7.2 | 13.4% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947 | 1487096 = | 45 (0.780) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947 | = 1499458 | 34 (0.470) | 14 (0.190) | 10/278 | 7.3 | 32.4% | intergenic (+35/‑129) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 1499495 | 25 (0.350) | intergenic (+72/‑92) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||