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 82 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,741,299 | 0 | C | T | 66.7% | 11.5 / 11.5 | 18 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 66.7% | 16.1 / 10.4 | 18 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 66.7% | 12.1 / 15.1 | 18 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | C | 66.7% | 34.1 / 19.0 | 18 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 60.0% | 8.9 / 42.3 | 45 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,725 | 0 | A | G | 57.1% | 8.0 / 37.8 | 35 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,741,274 | 0 | A | C | 57.1% | ‑0.3 / 10.6 | 14 | intergenic (+465/+287) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,348,749 | 0 | A | G | 54.8% | 0.6 / 46.1 | 42 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 2,282,817 | 0 | G | C | 53.8% | ‑5.8 / 12.1 | 13 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,818 | 0 | G | C | 53.8% | ‑5.6 / 12.3 | 13 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 195,634 | 0 | C | T | 52.5% | 6.0 / 74.1 | 59 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,282,822 | 0 | C | A | 50.0% | ‑0.1 / 14.0 | 14 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,741,273 | 1 | . | C | 42.9% | ‑3.9 / 24.8 | 14 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,275 | 0 | A | G | 42.9% | ‑2.5 / 11.4 | 14 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,842,949 | 1 | . | G | 42.9% | 4.0 / 39.4 | 21 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 2,669,714 | 0 | T | G | 41.7% | 4.0 / 26.8 | 24 | intergenic (+38/+37) | prpD/acnB | 2‑methylcitrate dehydratase/aconitate hydratase B |
| * | NC_002947 | 4,842,941 | 0 | C | . | 38.9% | 28.2 / 23.7 | 18 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 322,142 | 0 | T | C | 38.1% | 8.4 / 17.4 | 21 | intergenic (+427/+31) | aguA/PP_0267 | agmatine deiminase/ferric siderophore receptor |
| * | NC_002947 | 968,878 | 0 | G | T | 36.4% | 19.5 / 12.0 | 22 | intergenic (‑308/+23) | PP_0831/PP_t68 | hypothetical protein/tRNA‑Leu |
| * | NC_002947 | 2,669,717 | 0 | C | A | 36.4% | 23.8 / 16.4 | 22 | intergenic (+41/+34) | prpD/acnB | 2‑methylcitrate dehydratase/aconitate hydratase B |
| Marginal new junction evidence (lowest skew 10 of 108 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 6060500 | 36 (1.240) | 6 (0.230) | 6/236 | 2.5 | 16.2% | intergenic (+80/+101) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein |
| ? | NC_002947 | = 6060559 | 30 (1.160) | intergenic (+139/+42) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 5743404 | 30 (1.040) | 6 (0.230) | 6/238 | 2.5 | 17.6% | intergenic (‑181/+66) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase |
| ? | NC_002947 | = 5743432 | 29 (1.110) | intergenic (‑209/+38) | fbp/glgP | class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase | |||||
| * | ? | NC_002947 | = 90344 | 34 (1.180) | 7 (0.250) | 7/260 | 2.5 | 15.8% | intergenic (+19/+103) | PP_0079/PP_0080 | transcriptional regulator/hypothetical protein |
| ? | NC_002947 | = 90427 | 41 (1.440) | intergenic (+102/+20) | PP_0079/PP_0080 | transcriptional regulator/hypothetical protein | |||||
| * | ? | NC_002947 | = 857870 | 40 (1.380) | 6 (0.220) | 6/254 | 2.7 | 13.6% | coding (957/1443 nt) | phr | deoxyribodipyrimidine photolyase |
| ? | NC_002947 | = 857914 | 38 (1.370) | coding (913/1443 nt) | phr | deoxyribodipyrimidine photolyase | |||||
| * | ? | NC_002947 | = 5903825 | 29 (1.000) | 6 (0.220) | 5/244 | 2.9 | 14.8% | intergenic (+25/+82) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease |
| ? | NC_002947 | = 5903887 | 42 (1.570) | intergenic (+87/+20) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease | |||||
| * | ? | NC_002947 | 5501205 = | 32 (1.110) | 5 (0.190) | 5/242 | 2.9 | 14.4% | coding (623/855 nt) | PP_4834 | SPFH domain‑containing protein |
| ? | NC_002947 | 5501244 = | 30 (1.130) | coding (662/855 nt) | PP_4834 | SPFH domain‑containing protein | |||||
| * | ? | NC_002947 | 5257895 = | 34 (1.180) | 6 (0.220) | 5/246 | 2.9 | 13.1% | intergenic (‑46/+98) | PP_4634/PP_4635 | alpha/beta family hydrolase/trans‑2‑enoyl‑CoA reductase |
| ? | NC_002947 | 5257986 = | 48 (1.780) | intergenic (‑137/+7) | PP_4634/PP_4635 | alpha/beta family hydrolase/trans‑2‑enoyl‑CoA reductase | |||||
| * | ? | NC_002947 | 5099995 = | 22 (0.760) | 4 (0.170) | 4/214 | 2.9 | 19.6% | intergenic (+33/+120) | PP_4488/phhR | hypothetical protein/sigma‑54 dependent transcriptional regulator |
| ? | NC_002947 | 5100077 = | 15 (0.640) | intergenic (+115/+38) | PP_4488/phhR | hypothetical protein/sigma‑54 dependent transcriptional regulator | |||||
| * | ? | NC_002947 | 1443111 = | 31 (1.070) | 4 (0.170) | 4/214 | 2.9 | 18.6% | intergenic (‑42/+134) | ghrB/PP_1262 | 2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator |
| ? | NC_002947 | 1443179 = | 10 (0.430) | intergenic (‑110/+66) | ghrB/PP_1262 | 2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | 5916652 = | 26 (0.900) | 5 (0.180) | 5/256 | 3.0 | 15.8% | coding (231/1143 nt) | argE | acetylornithine deacetylase |
| ? | NC_002947 | 5916704 = | 28 (1.000) | coding (179/1143 nt) | argE | acetylornithine deacetylase | |||||