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 25 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,348,705 | 0 | A | G | 57.8% | 21.3 / 131.7 | 116 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,121 | 0 | C | T | 44.7% | 76.9 / 140.8 | 114 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,722 | 0 | A | G | 43.0% | 34.7 / 88.8 | 79 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 38.3% | 95.7 / 106.0 | 107 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,282,775 | 0 | G | C | 30.0% | 90.4 / 53.7 | 70 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,770 | 0 | T | G | 29.7% | 65.5 / 63.2 | 74 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,779 | 0 | C | A | 29.7% | 86.7 / 51.3 | 75 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 196,390 | 0 | T | C | 28.9% | 125.8 / 62.5 | 90 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,282,774 | 0 | G | C | 28.6% | 94.9 / 52.9 | 70 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 195,559 | 0 | C | A | 28.4% | 148.1 / 54.6 | 81 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,351 | 0 | C | G | 27.5% | 214.9 / 91.2 | 131 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,740,457 | 0 | G | A | 25.6% | 57.8 / 19.9 | 41 | intergenic (+22/+49) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,740,467 | 0 | T | G | 25.0% | 36.0 / 27.1 | 44 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,740,470 | 0 | A | T | 24.4% | 64.8 / 25.2 | 47 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 1,544,504 | 0 | T | G | 24.3% | 60.9 / 17.3 | 37 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 5,740,471 | 0 | A | T | 23.9% | 71.1 / 22.6 | 47 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,740,474 | 0 | C | A | 22.9% | 83.7 / 26.3 | 48 | intergenic (+39/+32) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 1,544,489 | 0 | C | A | 22.6% | 51.4 / 14.6 | 31 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 196,327 | 0 | A | C | 21.3% | 276.6 / 69.0 | 137 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,494 | 0 | C | G | 20.6% | 66.0 / 10.3 | 34 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| Marginal new junction evidence (lowest skew 10 of 498 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4586034 = | 40 (0.570) | 14 (0.240) | 14/238 | 4.6 | 36.0% | intergenic (+117/+98) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586105 = | 16 (0.270) | intergenic (+188/+27) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4808179 | 5 (0.070) | 23 (0.360) | 13/258 | 5.4 | 36.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 76 (1.180) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808179 | 5 (0.070) | 19 (0.310) | 10/242 | 6.1 | 42.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988949 | 47 (0.780) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652782 | 65 (0.920) | 12 (0.200) | 10/242 | 6.1 | 29.7% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808159 | 1 (0.020) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 611510 | NA (NA) | 13 (0.190) | 10/268 | 6.7 | NA | coding (407/966 nt) | PP_0526 | transposase |
| ? | NC_002947 | = 611525 | NA (NA) | coding (422/966 nt) | PP_0526 | transposase | |||||
| * | ? | NC_002947 | = 6060444 | 85 (1.200) | 14 (0.220) | 9/254 | 6.8 | 16.3% | intergenic (+80/+101) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein |
| ? | NC_002947 | = 6060503 | 67 (1.050) | intergenic (+139/+42) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947 | 4647557 = | 46 (0.650) | 6 (0.120) | 6/204 | 6.8 | 15.8% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647665 = | 31 (0.610) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | 967850 = | 63 (0.890) | 9 (0.140) | 9/252 | 6.8 | 13.7% | intergenic (‑29/+139) | PP_0830/PP_0831 | acetyltransferase/hypothetical protein |
| ? | NC_002947 | 967941 = | 57 (0.900) | intergenic (‑120/+48) | PP_0830/PP_0831 | acetyltransferase/hypothetical protein | |||||
| * | ? | NC_002947 | = 176399 | NA (NA) | 19 (0.280) +CGAAA |
10/272 | 6.8 | 19.0% | intergenic (+43/‑420) | PP_5SA/PP_16SB | 5S ribosomal RNA/16S ribosomal RNA |
| ? | NC_002947 | = 182013 | 84 (1.190) | intergenic (+2/+63) | PP_5SB/PP_0160 | 5S ribosomal RNA/ferrioxamine receptor | |||||
| * | ? | NC_002947 | = 3516176 | 77 (1.090) | 9 (0.130) | 9/270 | 7.2 | 10.8% | intergenic (+216/‑919) | PP_5576/PP_5578 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 3516185 | 75 (1.110) | intergenic (+225/‑910) | PP_5576/PP_5578 | hypothetical protein/hypothetical protein | |||||