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 25 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 68.4% | 34.4 / 16.4 | 19 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 64.7% | 28.7 / 16.2 | 19 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 61.5% | 6.4 / 99.7 | 91 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,338,608 | 0 | G | T | 55.6% | 3.4 / 11.1 | 10 | intergenic (+121/+21) | PP_3812/PP_5632 | lipase/allo‑isoleucine metabolism protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 53.8% | ‑0.3 / 100.7 | 78 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 42.9% | 21.2 / 11.0 | 29 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 1,544,504 | 0 | T | G | 41.7% | 3.7 / 14.9 | 12 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 40.2% | 92.7 / 131.1 | 98 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 37.5% | 111.7 / 103.9 | 104 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,327 | 0 | A | C | 36.6% | 120.1 / 132.4 | 101 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,306 | 0 | T | C | 34.9% | 125.9 / 102.3 | 108 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,754,681 | 0 | C | T | 34.3% | 38.1 / 26.0 | 35 | C30C (TGC→TGT) | PP_1557 | hypothetical protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 33.3% | 56.7 / 51.2 | 60 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 32.5% | 98.8 / 72.5 | 83 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,991,720 | 0 | T | C | 31.5% | 60.5 / 41.9 | 54 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947_CJ‑RC | 5,991,726 | 0 | A | . | 30.9% | 125.8 / 62.8 | 55 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947_CJ‑RC | 5,991,709 | 0 | C | T | 30.2% | 57.5 / 30.5 | 44 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947_CJ‑RC | 5,991,710 | 0 | A | G | 29.5% | 52.1 / 32.3 | 44 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 26.7% | 154.8 / 46.4 | 75 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,991,704 | 0 | C | A | 26.1% | 102.5 / 30.4 | 46 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 652782 | 63 (1.220) | 14 (0.320) | 12/240 | 3.3 | 34.2% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 0 (0.000) | 11 (0.230) | 10/256 | 4.1 | 34.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 41 (0.870) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.020) | 10 (0.200) +CGGG |
10/272 | 4.4 | 91.1% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 1 (0.020) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 0 (0.000) | 6 (0.140) | 5/240 | 5.7 | 27.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 31 (0.700) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 478261 = | 12 (0.230) | 4 (0.100) | 4/220 | 5.8 | 23.9% | 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_CJ‑RC | 478356 = | 16 (0.390) | 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_CJ‑RC | = 5114283 | 32 (0.620) | 4 (0.090) | 4/236 | 6.2 | 15.1% | intergenic (‑169/+97) | rluB/PP_4497 | 23S rRNA pseudouridylate synthase B/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 5114344 | 18 (0.410) | intergenic (‑230/+36) | rluB/PP_4497 | 23S rRNA pseudouridylate synthase B/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 182013 | 42 (0.810) | 4 (0.080) +TTTCG |
4/270 | 6.8 | 9.0% | intergenic (+2/+63) | PP_5SB/PP_0160 | 5S ribosomal RNA/ferrioxamine receptor |
| ? | NC_002947_CJ‑RC | = 1330512 | NA (NA) | intergenic (+43/‑264) | PP_5SE/PP_1157 | 5S ribosomal RNA/acetolactate synthase | |||||
| * | ? | NC_002947_CJ‑RC | 295071 = | 65 (1.260) | 3 (0.060) | 3/262 | 7.3 | 4.6% | coding (475/813 nt) | ssuB | aliphatic sulfonates ABC transporter ATP‑binding protein SsuB |
| ? | NC_002947_CJ‑RC | = 295067 | 65 (1.340) | coding (471/813 nt) | ssuB | aliphatic sulfonates ABC transporter ATP‑binding protein SsuB | |||||