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 66 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,722 | 0 | A | G | 51.4% | 0.3 / 90.8 | 70 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 46.7% | 57.7 / 155.6 | 122 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,327,121 | 0 | C | T | 42.1% | 75.5 / 123.7 | 108 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 40.7% | 80.9 / 126.4 | 113 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,740,467 | 0 | T | G | 37.8% | 23.9 / 41.0 | 45 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,988,911 | 0 | A | . | 34.7% | 159.4 / 94.1 | 73 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 955,155 | 0 | C | T | 34.6% | 77.9 / 66.7 | 83 | intergenic (+109/‑204) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 4,796,617 | 0 | G | C | 34.0% | 56.6 / 45.2 | 53 | intergenic (‑175/+43) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947 | 4,796,619 | 0 | A | G | 34.0% | 55.3 / 42.5 | 53 | intergenic (‑177/+41) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947 | 955,151 | 0 | G | A | 33.8% | 86.0 / 64.9 | 84 | intergenic (+105/‑208) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 5,988,905 | 0 | T | C | 32.4% | 86.7 / 61.2 | 74 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 955,153 | 0 | T | C | 31.8% | 99.3 / 66.8 | 85 | intergenic (+107/‑206) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 4,340,075 | 0 | A | T | 31.7% | 38.5 / 25.8 | 45 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 195,559 | 0 | C | A | 31.4% | 143.7 / 66.9 | 86 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,796,614 | 0 | G | C | 31.1% | 59.9 / 30.3 | 46 | intergenic (‑172/+46) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947 | 955,149 | 0 | A | G | 30.9% | 110.5 / 65.2 | 85 | intergenic (+103/‑210) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 955,152 | 0 | T | A | 30.9% | 98.8 / 68.1 | 85 | intergenic (+106/‑207) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 5,740,471 | 0 | A | T | 30.9% | 39.0 / 30.9 | 44 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 4,796,612 | 0 | C | T | 30.4% | 55.7 / 32.8 | 46 | intergenic (‑170/+48) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947 | 196,390 | 0 | T | C | 30.3% | 99.6 / 55.5 | 76 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 512 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 1487006 = | 55 (0.840) | 11 (0.220) | 10/214 | 4.8 | 18.8% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947 | 1487096 = | 52 (1.020) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947 | = 2957080 | 56 (0.860) | 12 (0.190) | 12/264 | 5.3 | 20.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947 | 2957165 = | 41 (0.650) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947 | 478261 = | 58 (0.890) | 7 (0.140) | 7/214 | 6.0 | 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 | 478356 = | 41 (0.810) | 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 | 5594092 = | 47 (0.720) | 7 (0.140) | 7/218 | 6.1 | 15.3% | intergenic (‑39/+106) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase |
| ? | NC_002947 | 5594185 = | 40 (0.770) | intergenic (‑132/+13) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||
| * | ? | NC_002947 | 5477090 = | 49 (0.750) | 7 (0.150) | 5/192 | 6.4 | 18.8% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5477189 = | 26 (0.570) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | 1297198 = | NA (NA) | 10 (0.160) | 9/264 | 6.4 | NA | coding (386/1329 nt) | PP_1133 | transposase |
| ? | NC_002947 | 1297218 = | NA (NA) | coding (406/1329 nt) | PP_1133 | transposase | |||||
| * | ? | NC_002947 | = 1970739 | 49 (0.750) | 8 (0.140) | 7/234 | 6.5 | 16.5% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1970801 | 39 (0.700) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947 | = 1499458 | 36 (0.550) | 13 (0.200) | 9/270 | 6.5 | 30.1% | intergenic (+35/‑129) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 1499495 | 25 (0.390) | intergenic (+72/‑92) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | = 699672 | 128 (1.970) | 7 (0.140) +29 bp |
6/216 | 6.5 | 8.7% | intergenic (+65/‑179) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| ? | NC_002947 | 5310821 = | 59 (0.910) | intergenic (‑232/+3) | PP_23SG/PP_t51 | 23S ribosomal RNA/tRNA‑Ala | |||||
| * | ? | NC_002947 | = 5914184 | 60 (0.920) | 9 (0.170) | 6/218 | 6.6 | 18.8% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | = 5914224 | 30 (0.580) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||