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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 34 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 | 1,070,246 | 1 | . | G | 66.7% | 41.8 / 24.5 | 25 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
* | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 65.0% | ‑0.7 / 10.9 | 22 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
* | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 64.0% | 42.6 / 29.2 | 25 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
* | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 60.0% | 81.9 / 153.7 | 141 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 4,338,608 | 0 | G | T | 54.5% | 13.4 / 28.3 | 22 | intergenic (+121/+21) | PP_3812/PP_5632 | lipase/allo‑isoleucine metabolism protein |
* | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 53.6% | 35.7 / 217.1 | 154 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 52.4% | 8.0 / 24.9 | 22 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
* | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 47.6% | 0.9 / 15.8 | 23 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
* | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 47.3% | 48.6 / 159.4 | 111 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
* | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 43.6% | 73.9 / 131.8 | 111 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
* | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 38.1% | 21.7 / 10.7 | 45 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
* | NC_002947_CJ‑RC | 1,544,359 | 0 | C | G | 34.2% | 61.9 / 14.6 | 38 | A388G (GCG→GGG) | mdfA | multidrug MFS transporter |
* | NC_002947_CJ‑RC | 4,740,951 | 0 | C | G | 33.3% | 13.0 / 11.5 | 18 | intergenic (+81/+672) | gltA/yeiW | citrate synthase/putative oxidoreductase |
* | NC_002947_CJ‑RC | 3,975,989 | 0 | T | G | 30.4% | 120.8 / 11.5 | 56 | P293P (CCA→CCC) | PP_3506 | magnesium chelatase subunit ChII |
* | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 29.1% | 95.1 / 10.6 | 55 | E610A (GAG→GCG) | betT‑I | choline transporter |
* | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 28.6% | 151.6 / 58.8 | 81 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
* | NC_002947_CJ‑RC | 3,578,433 | 0 | G | T | 28.6% | 78.2 / 36.5 | 57 | intergenic (+110/‑214) | PP_3158/PP_5589 | hypothetical protein/rhs repeat‑associated core domain‑containing protein |
* | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 28.2% | 55.8 / 22.8 | 39 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
* | NC_002947_CJ‑RC | 4,433,580 | 0 | G | C | 28.0% | 95.2 / 23.4 | 50 | intergenic (‑29/‑89) | PP_5648/PP_3928 | hypothetical protein/hypothetical protein |
* | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 27.0% | 179.3 / 103.9 | 115 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
Marginal new junction evidence (lowest skew 10 of 24 shown) | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_002947_CJ‑RC | = 2957080 | 41 (0.530) | 26 (0.350) | 23/282 | 3.9 | 36.0% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
? | NC_002947_CJ‑RC | 2957165 = | 53 (0.710) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
* | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 14 (0.180) +GCC |
14/286 | 6.4 | 93.5% | 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 | = 652782 | 60 (0.780) | 12 (0.180) | 11/252 | 6.6 | 31.7% | 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) | 12 (0.170) | 11/268 | 7.0 | 37.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | 5991580 = | 37 (0.520) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | 1737987 = | 102 (1.320) | 12 (0.180) | 10/258 | 7.2 | 12.4% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
? | NC_002947_CJ‑RC | = 1777401 | 80 (1.170) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
* | ? | NC_002947_CJ‑RC | = 1780066 | 17 (0.220) | 8 (0.110) | 8/278 | 8.6 | 33.9% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
? | NC_002947_CJ‑RC | 1780129 = | 15 (0.200) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
* | ? | NC_002947_CJ‑RC | = 5684230 | 3 (0.040) | 8 (0.110) +CGGG |
8/284 | 8.8 | 73.3% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
? | NC_002947_CJ‑RC | 5684231 = | 3 (0.040) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
* | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 10 (0.150) | 6/252 | 9.0 | 25.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | = 5991764 | 54 (0.810) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 4647702 | 19 (0.250) | 4 (0.070) | 4/214 | 9.0 | 20.6% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
? | NC_002947_CJ‑RC | = 4647732 | 17 (0.300) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
* | ? | NC_002947_CJ‑RC | = 2472115 | 14 (0.180) | 7 (0.100) | 7/278 | 9.2 | 13.8% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
? | NC_002947_CJ‑RC | 2472313 = | 74 (1.010) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase |