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 79 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,332,076 | 0 | C | T | 73.3% | 81.7 / 56.4 | 90 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,746,226 | 0 | C | T | 70.8% | 30.9 / 11.3 | 24 | intergenic (+468/+284) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,746,229 | 0 | C | T | 66.7% | 25.1 / 14.5 | 24 | intergenic (+471/+281) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,746,247 | 1 | . | T | 57.7% | 48.8 / 37.4 | 26 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,746,251 | 0 | A | G | 57.7% | 8.8 / 25.9 | 26 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,746,254 | 0 | A | . | 57.7% | 6.5 / 47.8 | 26 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,746,222 | 1 | . | C | 54.2% | 39.4 / 39.7 | 24 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,746,224 | 0 | A | G | 54.2% | 1.8 / 25.7 | 24 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,353,698 | 0 | A | G | 50.0% | 1.8 / 92.0 | 69 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,725 | 0 | A | G | 49.1% | 5.8 / 67.6 | 54 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,746,223 | 0 | A | C | 45.8% | 2.4 / 25.0 | 24 | intergenic (+465/+287) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,746,248 | 0 | C | T | 42.3% | 9.1 / 25.6 | 26 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,746,250 | 0 | A | C | 42.3% | 7.3 / 28.0 | 26 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,746,253 | 0 | C | G | 42.3% | 15.9 / 27.1 | 26 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 5,993,910 | 0 | T | C | 40.7% | 75.4 / 91.6 | 86 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,993,916 | 0 | A | . | 38.3% | 163.2 / 115.9 | 81 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 2,942,760 | 0 | A | T | 37.5% | 10.4 / 14.3 | 16 | L429L (CTT→CTA) ‡ | PP_2570 | transposase |
| * | NC_002947 | 2,942,761 | 0 | A | C | 37.5% | 9.6 / 12.3 | 16 | L429R (CTT→CGT) ‡ | PP_2570 | transposase |
| * | NC_002947 | 196,390 | 0 | T | C | 36.0% | 64.3 / 45.0 | 50 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,351 | 0 | C | G | 35.8% | 93.5 / 72.6 | 67 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 595 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4898573 | 62 (1.260) | 12 (0.310) | 11/202 | 2.9 | 18.1% | intergenic (+54/‑154) | pyk/PP_4302 | pyruvate kinase/urea transporter |
| ? | NC_002947 | = 4898598 | 60 (1.550) | intergenic (+79/‑129) | pyk/PP_4302 | pyruvate kinase/urea transporter | |||||
| * | ? | NC_002947 | = 380858 | 76 (1.550) | 15 (0.370) | 11/210 | 3.0 | 21.4% | intergenic (+45/+64) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer |
| ? | NC_002947 | = 380892 | 48 (1.200) | intergenic (+79/+30) | gbcB/PP_0317 | glycine‑betaine dioxygenase subunit/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947 | = 528049 | 7 (0.140) | 20 (0.430) | 13/242 | 3.1 | 75.1% | noncoding (1284/2902 nt) | PP_23SC | 23S ribosomal RNA |
| ? | NC_002947 | = 701118 | NA (NA) | noncoding (1265/2902 nt) | PP_23SD | 23S ribosomal RNA | |||||
| * | ? | NC_002947 | = 174474 | NA (NA) | 20 (0.430) | 13/242 | 3.1 | NA | noncoding (1272/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | NC_002947 | = 174479 | NA (NA) | noncoding (1277/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | NC_002947 | 5645236 = | 48 (0.980) | 9 (0.250) | 9/188 | 3.2 | 20.4% | intergenic (+8/‑102) | PP_4950/PP_4951 | hypothetical protein/EmrB/QacA family drug resistance transporter |
| ? | NC_002947 | 5645320 = | 35 (0.970) | intergenic (+92/‑18) | PP_4950/PP_4951 | hypothetical protein/EmrB/QacA family drug resistance transporter | |||||
| * | ? | NC_002947 | 4857407 = | 23 (0.470) | 10 (0.300) | 8/174 | 3.2 | 34.7% | intergenic (‑84/+213) | recR/ybaB | recombination protein RecR/nucleoid‑associated broad specificity regulator |
| ? | NC_002947 | 4857548 = | 22 (0.660) | intergenic (‑225/+72) | recR/ybaB | recombination protein RecR/nucleoid‑associated broad specificity regulator | |||||
| * | ? | NC_002947 | = 883865 | 32 (0.650) | 12 (0.330) | 9/192 | 3.2 | 42.1% | intergenic (+100/‑228) | PP_0766/PP_0767 | hypothetical protein/LuxR family transcriptional regulator |
| ? | NC_002947 | = 883875 | 9 (0.250) | intergenic (+110/‑218) | PP_0766/PP_0767 | hypothetical protein/LuxR family transcriptional regulator | |||||
| * | ? | NC_002947 | = 5164773 | 71 (1.450) | 9 (0.240) | 9/194 | 3.3 | 13.9% | intergenic (+39/+67) | PP_4542/PP_4543 | ABC transporter ATP‑binding protein/permease/hypothetical protein |
| ? | NC_002947 | = 5164788 | 58 (1.560) | intergenic (+54/+52) | PP_4542/PP_4543 | ABC transporter ATP‑binding protein/permease/hypothetical protein | |||||
| * | ? | NC_002947 | 478264 = | 77 (1.570) | 11 (0.290) | 9/196 | 3.3 | 15.4% | intergenic (+9/+101) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase |
| ? | NC_002947 | 478359 = | 62 (1.660) | intergenic (+104/+6) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase | |||||
| * | ? | NC_002947 | = 1736181 | 44 (0.900) | 9 (0.240) | 9/200 | 3.4 | 20.2% | intergenic (‑103/+88) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947 | = 1736217 | 37 (0.970) | intergenic (‑139/+52) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||