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 79 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,741,273 | 1 | . | C | 73.7% | 43.2 / 13.5 | 19 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 61.9% | 13.3 / 15.1 | 22 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,298 | 1 | . | T | 59.1% | 40.8 / 27.8 | 22 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 59.1% | 9.2 / 36.4 | 22 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 699,725 | 0 | A | G | 58.6% | 14.7 / 64.1 | 58 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,127 | 0 | C | T | 52.4% | 17.9 / 108.5 | 84 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,749 | 0 | A | G | 50.0% | 4.3 / 98.1 | 74 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 46.0% | 32.6 / 119.5 | 100 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,741,299 | 0 | C | T | 40.9% | 14.1 / 14.3 | 22 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 40.9% | 8.4 / 19.6 | 22 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 38.1% | 19.2 / 17.2 | 22 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 5,545,210 | 0 | A | T | 37.5% | 8.1 / 14.1 | 16 | intergenic (‑302/+575) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB |
| * | NC_002947 | 5,545,211 | 0 | A | C | 37.5% | 8.0 / 13.5 | 16 | intergenic (‑303/+574) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB |
| * | NC_002947 | 4,951,018 | 0 | C | A | 35.3% | 39.1 / 21.0 | 34 | intergenic (‑123/+34) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
| * | NC_002947 | 5,545,209 | 0 | G | T | 33.3% | 14.8 / 11.4 | 18 | intergenic (‑301/+576) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB |
| * | NC_002947 | 5,988,961 | 0 | T | C | 33.3% | 93.2 / 57.4 | 75 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,951,017 | 0 | T | G | 32.4% | 23.1 / 27.9 | 35 | intergenic (‑122/+35) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
| * | NC_002947 | 5,997,245 | 1 | . | G | 31.1% | 102.4 / 84.2 | 61 | intergenic (‑158/+42) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947 | 5,997,250 | 0 | C | . | 31.1% | 136.4 / 68.7 | 62 | intergenic (‑163/+37) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947 | 322,142 | 0 | T | C | 30.8% | 57.7 / 37.5 | 52 | intergenic (+427/+31) | aguA/PP_0267 | agmatine deiminase/ferric siderophore receptor |
| Marginal new junction evidence (lowest skew 10 of 528 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 511921 | 62 (1.240) | 12 (0.270) | 12/238 | 2.7 | 18.2% | intergenic (+58/‑90) | trpC/PP_0423 | indole‑3‑glycerol phosphate synthase/hypothetical protein |
| ? | NC_002947 | = 511969 | 53 (1.200) | intergenic (+106/‑42) | trpC/PP_0423 | indole‑3‑glycerol phosphate synthase/hypothetical protein | |||||
| * | ? | NC_002947 | = 359675 | 76 (1.520) | 14 (0.290) | 13/256 | 2.8 | 15.6% | intergenic (+32/+88) | gbdR/PP_0299 | AraC family transcriptional regulator/hypothetical protein |
| ? | NC_002947 | = 359721 | 79 (1.660) | intergenic (+78/+42) | gbdR/PP_0299 | AraC family transcriptional regulator/hypothetical protein | |||||
| * | ? | NC_002947 | 5125135 = | 89 (1.780) | 10 (0.250) | 10/216 | 2.9 | 12.2% | intergenic (+61/‑121) | PP_4511/PP_4512 | AraC family transcriptional regulator/DMT superfamily permease |
| ? | NC_002947 | 5125214 = | 72 (1.790) | intergenic (+140/‑42) | PP_4511/PP_4512 | AraC family transcriptional regulator/DMT superfamily permease | |||||
| * | ? | NC_002947 | 1436018 = | 57 (1.140) | 12 (0.250) | 12/256 | 3.0 | 18.8% | intergenic (‑48/+105) | PP_1256/PP_1257 | alpha‑ketoglutarate semialdehyde dehydrogenase/1‑pyrroline‑4‑hydroxy‑2‑carboxylate deaminase |
| ? | NC_002947 | 1436109 = | 49 (1.030) | intergenic (‑139/+14) | PP_1256/PP_1257 | alpha‑ketoglutarate semialdehyde dehydrogenase/1‑pyrroline‑4‑hydroxy‑2‑carboxylate deaminase | |||||
| * | ? | NC_002947 | 478264 = | 78 (1.560) | 9 (0.230) | 9/208 | 3.0 | 14.0% | 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 = | 50 (1.290) | 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 | = 5816927 | 38 (0.760) | 11 (0.250) | 10/232 | 3.1 | 23.7% | intergenic (+57/+72) | PP_5092/pilT | NLP/P60 protein/twitching motility protein |
| ? | NC_002947 | = 5816954 | 38 (0.880) | intergenic (+84/+45) | PP_5092/pilT | NLP/P60 protein/twitching motility protein | |||||
| * | ? | NC_002947 | 5903827 = | 62 (1.240) | 13 (0.300) | 10/236 | 3.2 | 19.0% | intergenic (+27/+80) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease |
| ? | NC_002947 | 5903887 = | 56 (1.270) | intergenic (+87/+20) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease | |||||
| * | ? | NC_002947 | 5759460 = | 70 (1.400) | 9 (0.240) | 8/204 | 3.2 | 17.3% | intergenic (+13/+143) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947 | 5759552 = | 33 (0.870) | intergenic (+105/+51) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947 | 5136162 = | 50 (1.000) | 11 (0.230) | 11/256 | 3.2 | 18.4% | coding (456/1566 nt) | PP_4521 | aerotaxis receptor |
| ? | NC_002947 | 5136215 = | 50 (1.050) | coding (403/1566 nt) | PP_4521 | aerotaxis receptor | |||||
| * | ? | NC_002947 | 4586063 = | 4 (0.080) | 7 (0.200) | 7/192 | 3.3 | 34.3% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586167 = | 24 (0.670) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||