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 28 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 | 56.6% | 21.5 / 87.0 | 76 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,121 | 0 | C | T | 55.3% | 15.6 / 165.5 | 132 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 54.7% | ‑3.0 / 161.9 | 129 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 45.4% | 62.2 / 145.5 | 119 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 195,559 | 0 | C | A | 29.7% | 166.9 / 64.8 | 91 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 197,590 | 0 | T | C | 28.6% | 155.2 / 75.8 | 105 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,911 | 0 | A | . | 25.8% | 245.5 / 89.7 | 99 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,530,026 | 0 | T | A | 24.7% | 103.7 / 36.1 | 73 | intergenic (+32/‑136) | PP_4018/topB | acetyltransferase/DNA topoisomerase III |
| * | NC_002947 | 445,105 | 0 | A | T | 24.5% | 95.8 / 17.5 | 53 | intergenic (+78/‑210) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 1,466,536 | 0 | C | A | 23.7% | 82.7 / 11.4 | 38 | G219C (GGC→TGC) | algG | poly(beta‑D‑mannuronate) C5 epimerase |
| * | NC_002947 | 1,544,501 | 0 | G | C | 23.6% | 95.1 / 24.9 | 55 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 5,988,905 | 0 | T | C | 23.5% | 177.0 / 51.9 | 98 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 197,572 | 0 | G | A | 23.4% | 199.0 / 60.2 | 111 | K1026K (AAG→AAA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,489 | 0 | C | A | 23.1% | 86.4 / 27.2 | 52 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 5,740,467 | 0 | T | G | 23.1% | 63.9 / 24.2 | 52 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 196,351 | 0 | C | G | 22.7% | 193.1 / 54.5 | 97 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,895 | 0 | A | G | 22.3% | 197.6 / 53.3 | 103 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 1,544,494 | 0 | C | G | 21.8% | 116.5 / 27.9 | 55 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 5,740,471 | 0 | A | T | 21.7% | 89.7 / 10.6 | 50 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 1,544,504 | 0 | T | G | 21.3% | 111.6 / 31.9 | 61 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| Marginal new junction evidence (lowest skew 10 of 546 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4586029 | 16 (0.210) | 22 (0.310) | 16/258 | 5.4 | 43.2% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586109 | 43 (0.600) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4808179 | 0 (0.000) | 28 (0.400) | 14/256 | 6.0 | 45.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 66 (0.930) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652782 | 50 (0.650) | 15 (0.230) | 12/240 | 6.3 | 41.2% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808159 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 4586034 = | 26 (0.340) | 12 (0.180) | 10/236 | 6.9 | 30.8% | intergenic (+117/+98) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586105 = | 32 (0.490) | intergenic (+188/+27) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 6149145 | 59 (0.760) | 12 (0.160) | 11/268 | 7.4 | 17.8% | intergenic (‑1329/‑1845) | PP_5393/PP_5395 | metal‑binding chaperone/hypothetical protein |
| ? | NC_002947 | = 6149156 | 54 (0.730) | intergenic (‑1340/‑1834) | PP_5393/PP_5395 | metal‑binding chaperone/hypothetical protein | |||||
| * | ? | NC_002947 | = 5858864 | 46 (0.590) | 8 (0.130) | 7/220 | 7.8 | 19.2% | intergenic (+42/+96) | PP_5134/PP_5135 | hypothetical protein/ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 5858909 | 31 (0.510) | intergenic (+87/+51) | PP_5134/PP_5135 | hypothetical protein/ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 5914184 | 64 (0.830) | 7 (0.110) | 7/224 | 7.9 | 12.8% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | = 5914224 | 44 (0.710) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | 100443 = | 86 (1.110) | 8 (0.120) | 8/246 | 8.1 | 9.7% | intergenic (‑35/+87) | PP_0094/PP_0095 | 5'‑nucleotidase/hypothetical protein |
| ? | NC_002947 | 100525 = | 74 (1.090) | intergenic (‑117/+5) | PP_0094/PP_0095 | 5'‑nucleotidase/hypothetical protein | |||||
| * | ? | NC_002947 | 3969585 = | NA (NA) | 10 (0.140) | 9/266 | 8.2 | NA | coding (220/321 nt) | PP_3499 | transposase |
| ? | NC_002947 | 3969623 = | NA (NA) | coding (258/321 nt) | PP_3499 | transposase | |||||
| * | ? | NC_002947 | 63722 = | 98 (1.260) | 9 (0.120) | 9/264 | 8.2 | 9.0% | coding (741/858 nt) | PP_0054 | membrane protein |
| ? | NC_002947 | 63778 = | 90 (1.230) | coding (797/858 nt) | PP_0054 | membrane protein | |||||