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 25 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 | 2 | . | A | 73.3% | 69.5 / 24.5 | 31 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
* | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 57.7% | ‑5.3 / 23.9 | 29 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
* | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 57.4% | 27.7 / 119.1 | 101 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 1,712,075 | 0 | G | T | 56.0% | ‑5.0 / 17.9 | 25 | intergenic (+66/‑192) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
* | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 54.5% | ‑6.3 / 12.1 | 11 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
* | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 52.0% | 52.0 / 251.7 | 174 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
* | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 50.0% | 30.3 / 206.0 | 134 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
* | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 43.8% | 29.4 / 13.9 | 35 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
* | NC_002947_CJ‑RC | 6,092,722 | 0 | G | T | 39.5% | 71.0 / 10.5 | 43 | R362R (CGG→CGT) | potF‑IV | putrescine‑binding protein |
* | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 34.9% | 134.8 / 116.3 | 130 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
* | NC_002947_CJ‑RC | 418,289 | 0 | C | A | 27.4% | 178.9 / 12.9 | 74 | F24L (TTC→TTA) | PP_0345 | heptose kinase WapP |
* | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 27.3% | 46.2 / 18.6 | 33 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
* | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 26.9% | 129.3 / 11.2 | 69 | E610A (GAG→GCG) | betT‑I | choline transporter |
* | NC_002947_CJ‑RC | 2,737,109 | 0 | T | G | 25.4% | 139.8 / 10.2 | 63 | V1336G (GTG→GGG) | PP_2394 | leucine‑rich repeat‑containing protein |
* | NC_002947_CJ‑RC | 1,404,018 | 0 | A | C | 25.4% | 137.9 / 10.1 | 67 | V555G (GTG→GGG) | PP_1228 | methyl‑accepting chemotaxis transducer |
* | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 24.8% | 181.6 / 67.9 | 109 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
* | NC_002947_CJ‑RC | 2,489,065 | 0 | T | G | 24.2% | 151.7 / 10.1 | 66 | V21G (GTG→GGG) | PP_2184 | formate dehydrogenase subunit beta |
* | NC_002947_CJ‑RC | 5,211,931 | 0 | A | G | 24.0% | 95.2 / 12.3 | 51 | intergenic (‑94/+84) | rnd/PP_4592 | ribonuclease D/metal dependent hydrolase |
* | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 23.4% | 248.3 / 103.6 | 141 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
* | NC_002947_CJ‑RC | 197,590 | 0 | T | C | 22.9% | 197.4 / 69.2 | 125 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
Marginal new junction evidence (lowest skew 10 of 23 shown) | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.060) | 24 (0.300) | 19/268 | 5.4 | 42.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
? | NC_002947_CJ‑RC | 5991580 = | 61 (0.770) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 2957080 | 47 (0.540) | 13 (0.160) | 13/282 | 7.9 | 23.6% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
? | NC_002947_CJ‑RC | 2957165 = | 39 (0.470) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
* | ? | NC_002947_CJ‑RC | = 5558423 | 6 (0.070) | 14 (0.170) +GCC |
13/286 | 8.0 | 70.4% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
? | NC_002947_CJ‑RC | 5558424 = | 6 (0.070) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
* | ? | NC_002947_CJ‑RC | = 2472115 | 31 (0.360) | 12 (0.150) | 11/278 | 8.6 | 19.4% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
? | NC_002947_CJ‑RC | 2472313 = | 70 (0.850) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
* | ? | NC_002947_CJ‑RC | = 1780066 | 16 (0.190) | 10 (0.120) | 10/278 | 9.0 | 36.2% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
? | NC_002947_CJ‑RC | 1780129 = | 20 (0.240) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
* | ? | NC_002947_CJ‑RC | 1737987 = | 116 (1.340) | 7 (0.090) | 7/258 | 9.9 | 6.8% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
? | NC_002947_CJ‑RC | = 1777401 | 89 (1.170) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
* | ? | NC_002947_CJ‑RC | 1114870 = | 36 (0.420) | 6 (0.080) | 6/242 | 10.0 | 16.5% | intergenic (‑64/+115) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
? | NC_002947_CJ‑RC | 1114946 = | 31 (0.430) | intergenic (‑140/+39) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||
* | ? | NC_002947_CJ‑RC | = 5991586 | 59 (0.680) | 6 (0.070) | 6/276 | 11.1 | 9.6% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
? | NC_002947_CJ‑RC | 5991778 = | 57 (0.700) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 5991572 | 72 (0.830) | 6 (0.070) | 6/276 | 11.1 | 8.2% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
? | NC_002947_CJ‑RC | 5991794 = | 66 (0.810) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
* | ? | NC_002947_CJ‑RC | = 5819686 | 20 (0.230) | 5 (0.070) | 5/256 | 11.1 | 29.0% | intergenic (+57/+72) | PP_5092/pilT | NLP/P60 protein/twitching motility protein |
? | NC_002947_CJ‑RC | = 5819713 | 7 (0.090) | intergenic (+84/+45) | PP_5092/pilT | NLP/P60 protein/twitching motility protein |