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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 29 shown, sorted by frequency from high to low) | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | NC_002947_CJ‑RC | 697,107 | 0 | T | G | 53.3% | 7.0 / 19.3 | 19 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
* | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 53.2% | 2.1 / 121.1 | 94 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 51.2% | 22.1 / 173.7 | 125 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
* | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 48.0% | 88.3 / 212.8 | 155 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 5,923,026 | 0 | A | C | 43.2% | 39.8 / 12.9 | 38 | K266T (AAG→ACG) | PP_5190 | type II secretion system protein |
* | NC_002947_CJ‑RC | 697,138 | 0 | C | G | 39.1% | 22.3 / 11.5 | 23 | intergenic (+65/‑686) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
* | NC_002947_CJ‑RC | 5,442,128 | 0 | G | C | 36.7% | 40.4 / 15.4 | 30 | R15G (CGG→GGG) | rluE | 23S rRNA pseudouridine(2457) synthase |
* | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 33.3% | 11.8 / 18.3 | 21 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
* | NC_002947_CJ‑RC | 1,615,716 | 0 | G | C | 31.4% | 56.5 / 10.7 | 35 | T12T (ACC→ACG) | PP_1415 | membrane protein |
* | NC_002947_CJ‑RC | 3,597,526 | 0 | C | G | 30.5% | 109.8 / 10.9 | 59 | A196P (GCC→CCC) | PP_3174 | oxidoreductase |
* | NC_002947_CJ‑RC | 2,282,779 | 0 | C | A | 30.0% | 29.4 / 12.4 | 20 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
* | NC_002947_CJ‑RC | 1,403,591 | 0 | T | C | 28.6% | 27.8 / 17.9 | 32 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
* | NC_002947_CJ‑RC | 4,140,143 | 0 | G | C | 27.5% | 153.3 / 13.8 | 69 | intergenic (+35/‑230) | PP_3644/PP_5609 | monooxygenase subunit/hypothetical protein |
* | NC_002947_CJ‑RC | 1,403,590 | 0 | G | A | 26.7% | 36.9 / 14.3 | 30 | intergenic (‑56/+25) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
* | NC_002947_CJ‑RC | 3,975,989 | 0 | T | G | 25.0% | 103.3 / 13.4 | 48 | P293P (CCA→CCC) | PP_3506 | magnesium chelatase subunit ChII |
* | NC_002947_CJ‑RC | 1,497,831 | 0 | T | G | 23.6% | 145.5 / 11.5 | 72 | V140G (GTC→GGC) | PP_1310 | hypothetical protein |
* | NC_002947_CJ‑RC | 4,029,540 | 0 | A | C | 23.5% | 180.5 / 13.9 | 81 | A306A (GCA→GCC) | PP_3553 | AMP‑binding domain‑containing protein |
* | NC_002947_CJ‑RC | 197,632 | 0 | T | C | 23.2% | 117.2 / 38.2 | 69 | T1046T (ACT→ACC) | PP_0168 | putative surface adhesion protein |
* | NC_002947_CJ‑RC | 955,153 | 0 | T | C | 22.9% | 64.2 / 13.1 | 35 | intergenic (+107/‑206) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
* | NC_002947_CJ‑RC | 2,192,477 | 0 | G | T | 22.8% | 141.6 / 12.5 | 57 | intergenic (+86/‑118) | PP_1937/PP_1938 | helicase/hypothetical protein |
Marginal new junction evidence (lowest skew 10 of 47 shown) | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.070) | 23 (0.410) | 15/222 | 4.3 | 54.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | = 5991750 | 34 (0.600) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 5991586 | 56 (0.750) | 14 (0.200) | 14/276 | 6.0 | 21.2% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
? | NC_002947_CJ‑RC | 5991778 = | 51 (0.720) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 18 (0.250) +GCC |
14/286 | 6.3 | 94.8% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
? | NC_002947_CJ‑RC | 5558424 = | 1 (0.010) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
* | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 11 (0.150) +CGGG |
11/284 | 7.3 | 91.9% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
? | NC_002947_CJ‑RC | 5684231 = | 1 (0.010) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
* | ? | NC_002947_CJ‑RC | = 2957080 | 40 (0.530) | 10 (0.140) | 10/282 | 7.7 | 19.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
? | NC_002947_CJ‑RC | 2957165 = | 44 (0.610) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
* | ? | NC_002947_CJ‑RC | = 652782 | 63 (0.840) | 7 (0.110) | 6/252 | 8.9 | 20.5% | 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 | 4 (0.050) | 6 (0.090) | 6/268 | 9.3 | 18.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | 5991580 = | 51 (0.740) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 2472140 | 21 (0.280) | 3 (0.050) | 3/214 | 9.6 | 13.2% | intergenic (+44/+105) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
? | NC_002947_CJ‑RC | = 2472186 | 24 (0.440) | intergenic (+90/+59) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase | |||||
* | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 4 (0.060) | 4/252 | 10.1 | 13.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | = 5991764 | 48 (0.740) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 6003747 | 20 (0.270) | 3 (0.050) | 3/232 | 10.2 | 14.0% | intergenic (+39/+70) | PP_5256/amaA | cyclic nucleotide‑binding protein/L‑pipecolate oxidase |
? | NC_002947_CJ‑RC | = 6003781 | 21 (0.350) | intergenic (+73/+36) | PP_5256/amaA | cyclic nucleotide‑binding protein/L‑pipecolate oxidase |