Sentence examples for minimum variant frequency from inspiring English sources

Heteroplasmic sites in NCRs were called with the "Find Variations/ SNPs" function in Geneious 7.0.5 with the parameters "Minimum Coverage" 50, and "Minimum Variant Frequency" 10%.

Variants were detected by Quality-based Variant Detection Tool using following parameters; neighborhood radius: 5, maximum gap and mismatch counts: 5, minimum neighborhood and central qualities: 30, minimum coverage: 10, minimum variant frequency: 10%, and maximum expected alleles: 4. Non-specific matches were ignored and bacterial genetic code was used.

To classify whether mismatches were sequencing errors or genomic variations, parameters were set as follows: minimum depth, 30; minimum variant frequency, 35%; least mismatch count, 20; and homo/heterozygote fold change, 2. RAP-DB was utilized to locate the discovered SNPs.

Minimum variant frequency was set to zero, to allow comparison with ShoRAH.

SNP calling parameters were set to minimum coverage = 5, and minimum variant frequency = 0.2.

Sanger sequencing confirmed that none of the SNPs detected at a minimum variant frequency of 10-20% was real.

To determine the most appropriate settings for each dataset, SNP detection was conducted twice with minimum variant frequencies (mvf) of 10%and20%0%.

For variant calling, MuTect45 version 1.1.4 (default settings) and VarScan46 version 2.2.8 were used; for VarScan somatic, minimum variant allele frequency in the tumor was set to 10%; following recommendations from VarScan developers, somatic single-nucleotide variants (SNV) calls were further filtered to remove potential false positives; finally only high confidence calls were retained.

Furthermore, the minimum variant allele frequency threshold for VarScan was set to, likewise for CRISP the number of haplotypes in each pool was set to 300.

At the sequencing depth of 50-fold, it has been estimated that >85% of somatic mutations with minimum variant allele frequency of 10% could be detected.

A position to make a call, the following criteria have to be satisfied: (1) minimum read depth (2)minimum number of reads with variant allele (3) minimum variant allele frequency (4) minimum base quality (5) max p value.