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 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,348,705 | 0 | A | G | 62.3% | 53.8 / 110.6 | 114 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 51.7% | 13.2 / 155.9 | 120 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 699,722 | 0 | A | G | 51.1% | 1.1 / 122.7 | 94 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,121 | 0 | C | T | 42.1% | 80.4 / 128.7 | 117 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 195,559 | 0 | C | A | 41.8% | 77.3 / 87.2 | 80 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,351 | 0 | C | G | 27.6% | 119.2 / 62.2 | 87 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,485,162 | 0 | T | C | 26.9% | 33.2 / 11.4 | 26 | intergenic (+68/‑79) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 1,544,489 | 0 | C | A | 25.8% | 55.0 / 14.3 | 32 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,637,325 | 0 | A | T | 24.6% | 108.2 / 34.6 | 66 | intergenic (+34/+32) | pdxJ/PP_1437 | pyridoxine 5'‑phosphate synthase/heavy metal sensor histidine kinase |
| * | NC_002947 | 1,637,326 | 0 | A | T | 24.2% | 123.7 / 27.6 | 66 | intergenic (+35/+31) | pdxJ/PP_1437 | pyridoxine 5'‑phosphate synthase/heavy metal sensor histidine kinase |
| * | NC_002947 | 441,326 | 0 | G | . | 23.8% | 45.3 / 13.5 | 21 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947 | 4,049,910 | 0 | C | G | 23.8% | 70.5 / 19.5 | 42 | intergenic (+43/‑58) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| * | NC_002947 | 196,327 | 0 | A | C | 23.5% | 185.9 / 57.1 | 102 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 197,590 | 0 | T | C | 23.1% | 153.9 / 48.2 | 92 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,306 | 0 | T | C | 22.9% | 188.7 / 55.0 | 105 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,663,077 | 0 | A | T | 22.9% | 64.0 / 10.2 | 35 | intergenic (+23/+15) | purT/yhjE | phosphoribosylglycinamide formyltransferase/metabolite transport protein YhjE |
| * | NC_002947 | 4,796,619 | 0 | A | G | 22.4% | 90.4 / 19.9 | 50 | intergenic (‑177/+41) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947 | 1,544,494 | 0 | C | G | 22.2% | 70.7 / 14.4 | 36 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,130,192 | 0 | A | T | 21.7% | 77.6 / 21.1 | 46 | intergenic (‑247/+57) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947 | 2,282,770 | 0 | T | G | 21.6% | 71.0 / 24.7 | 53 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 620 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 5988771 | 5301 (80.180) | 156 (2.500) | 67/264 | 0.0 | 3.3% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5988963 = | 4239 (68.030) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5985492 | 4802 (72.630) | 103 (1.670) | 49/262 | 0.2 | 2.2% | coding (104/405 nt) | PP_5244 | AraC family transcriptional regulator |
| ? | NC_002947 | = 5985508 | 4551 (73.600) | coding (88/405 nt) | PP_5244 | AraC family transcriptional regulator | |||||
| * | ? | NC_002947 | = 5989993 | 5541 (83.810) | 144 (2.290) | 49/266 | 0.3 | 2.6% | intergenic (+305/+44) | PP_5247/ycaC‑III | hypothetical protein/putative hydrolase |
| ? | NC_002947 | = 5990003 | 5520 (87.920) | intergenic (+315/+34) | PP_5247/ycaC‑III | hypothetical protein/putative hydrolase | |||||
| * | ? | NC_002947 | = 5986153 | 5063 (76.580) | 156 (2.470) | 49/268 | 0.3 | 3.0% | coding (420/987 nt) | PP_5245 | AraC family transcriptional regulator |
| ? | NC_002947 | = 5986156 | 5089 (80.450) | coding (423/987 nt) | PP_5245 | AraC family transcriptional regulator | |||||
| * | ? | NC_002947 | = 5989280 | 5506 (83.280) | 86 (1.450) | 37/252 | 0.7 | 1.7% | noncoding (29/87 nt) | PP_mr64 | C4 ncRNA |
| ? | NC_002947 | = 5989327 | 5077 (85.400) | noncoding (76/87 nt) coding (38/399 nt) |
PP_mr64 PP_5247 |
C4 ncRNA hypothetical protein |
|||||
| * | ? | NC_002947 | = 5985353 | 5173 (78.250) | 98 (1.530) | 39/272 | 0.8 | 1.9% | coding (243/405 nt) | PP_5244 | AraC family transcriptional regulator |
| ? | NC_002947 | = 5985371 | 5197 (80.940) | coding (225/405 nt) | PP_5244 | AraC family transcriptional regulator | |||||
| * | ? | NC_002947 | 5988012 = | 4886 (73.910) | 97 (1.520) | 37/270 | 0.9 | 2.0% | coding (1094/1788 nt) | kefB‑III | glutathione‑regulated potassium/H+ antiporter |
| ? | NC_002947 | 5988042 = | 5000 (78.450) | coding (1124/1788 nt) | kefB‑III | glutathione‑regulated potassium/H+ antiporter | |||||
| * | ? | NC_002947 | 5985206 = | 5181 (78.370) | 110 (1.740) | 37/268 | 0.9 | 2.2% | coding (390/405 nt) | PP_5244 | AraC family transcriptional regulator |
| ? | NC_002947 | 5985245 = | 4861 (76.840) | coding (351/405 nt) | PP_5244 | AraC family transcriptional regulator | |||||
| * | ? | NC_002947 | 5984910 = | 4049 (61.240) | 105 (1.670) | 35/266 | 1.0 | 2.4% | coding (210/627 nt) | ycaC‑II | putative hydrolase |
| ? | NC_002947 | 5984947 = | 4783 (76.180) | coding (173/627 nt) | ycaC‑II | putative hydrolase | |||||
| * | ? | NC_002947 | 5989987 = | 5542 (83.830) | 104 (1.660) | 33/266 | 1.2 | 1.9% | intergenic (+299/+50) | PP_5247/ycaC‑III | hypothetical protein/putative hydrolase |
| ? | NC_002947 | 5990011 = | 5520 (87.920) | intergenic (+323/+26) | PP_5247/ycaC‑III | hypothetical protein/putative hydrolase | |||||