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 57 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 2,040,315 | 1 | . | G | 66.7% | 23.3 / 10.2 | 12 | coding (1130/1143 nt) | rffE | UDP‑N‑acetylglucosamine‑2‑epimerase |
| * | NC_002947 | 4,160,437 | 0 | A | C | 66.7% | 5.0 / 12.1 | 37 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947 | 4,350,671 | 0 | A | G | 66.7% | 40.2 / 67.4 | 75 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,511,866 | 0 | A | C | 61.1% | 2.2 / 11.5 | 38 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947 | 3,449,251 | 0 | A | C | 57.1% | 5.6 / 17.5 | 52 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947 | 5,511,875 | 0 | T | G | 56.7% | ‑0.3 / 10.9 | 37 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947 | 3,449,256 | 0 | T | G | 56.2% | ‑4.1 / 25.2 | 53 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947 | 1,114,888 | 0 | G | C | 54.5% | 4.4 / 11.7 | 11 | intergenic (‑77/+102) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| * | NC_002947 | 5,511,878 | 0 | T | G | 54.0% | ‑0.6 / 24.1 | 39 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| * | NC_002947 | 195,634 | 0 | C | T | 52.5% | ‑5.8 / 51.7 | 40 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 3,931,807 | 0 | A | C | 52.4% | 2.8 / 17.7 | 21 | W423G (TGG→GGG) | PP_5603 | FAD dependent oxidoreductase |
| * | NC_002947 | 3,031,248 | 0 | T | A | 51.6% | 25.7 / 38.4 | 34 | T312T (ACT→ACA) | pcaY | aromatic acid chemoreceptor |
| * | NC_002947 | 699,725 | 0 | A | G | 50.0% | ‑4.2 / 32.5 | 24 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,148,800 | 0 | T | G | 50.0% | 0.5 / 12.8 | 26 | T151P (ACG→CCG) | PP_1007 | transmembrane sensor |
| * | NC_002947 | 3,793,571 | 0 | T | G | 48.6% | ‑3.3 / 17.6 | 38 | D571A (GAC→GCC) | PP_3354 | acyl‑CoA dehydrogenase |
| * | NC_002947 | 195,559 | 0 | C | A | 46.9% | 9.2 / 35.5 | 33 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 923,649 | 0 | T | G | 41.4% | 69.9 / 19.4 | 58 | Q516P (CAG→CCG) | PP_0804 | protein secretion ABC transporter permease/ATP‑binding protein |
| * | NC_002947 | 1,590,985 | 0 | G | T | 40.5% | 49.4 / 11.3 | 37 | intergenic (+94/+30) | PP_1394/PP_1395 | acetolactate synthase large subunit/AraC family transcriptional regulator |
| * | NC_002947 | 2,357,176 | 0 | A | C | 40.5% | 63.2 / 15.7 | 42 | V267G (GTG→GGG) | PP_2069 | multidrug MFS transporter outer membrane protein |
| * | NC_002947 | 1,777,563 | 0 | A | C | 40.4% | 63.4 / 22.5 | 52 | intergenic (+255/+37) | PP_5476/PP_1585 | hypothetical protein/antidote protein |
| 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 | 1419553 = | 47 (0.890) | 13 (0.330) | 5/200 | 2.4 | 32.7% | intergenic (‑36/+101) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | 1419647 = | 18 (0.450) | intergenic (‑130/+7) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 5990749 | 124 (2.350) | 7 (0.140) | 6/248 | 2.6 | 6.9% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5990941 = | 73 (1.480) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4810141 = | 0 (0.000) | 7 (0.170) | 4/212 | 2.8 | 10.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5990757 = | 119 (2.820) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652786 | 46 (0.870) | 6 (0.160) | 3/194 | 3.0 | 26.2% | coding (1960/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | 4810176 = | 0 (0.000) | intergenic (‑318/‑237) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 5990646 | 131 (2.490) | 3 (0.060) | 3/250 | 3.6 | 3.0% | coding (1750/1788 nt) | kefB‑III | glutathione‑regulated potassium/H+ antiporter |
| ? | NC_002947 | 5990934 = | 71 (1.420) | intergenic (+250/‑296) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 2306946 = | 57 (1.080) | 3 (0.060) | 3/264 | 3.7 | 4.7% | coding (1576/1719 nt) | PP_2028 | TPR repeat‑containing protein |
| ? | NC_002947 | = 4018882 | 65 (1.230) | coding (818/1410 nt) | PP_3544 | GntR family transcriptional regulator | |||||