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The author used 20 lines combining one or more variant at these loci.
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In contrast, GATK called more variants at mid-frequency and showed higher overall heterozygosity levels.
Among subjects with one or more variants at both of the XPD polymorphisms, there was a 2-fold risk of SCC (OR = 2.2; 95% CI, 1.0 5.0) or those with high arsenic (> 0.286 μg/g) relative to those with lower arsenic.
The data pertain to three and four alleles at the major histocompatibility loci HLA-A and HLA-B respectively; the data, after a modification explained subsequently, are shown in Table 2. Frankham et al. (2010) presented only the data for these alleles, yet there are many more variants at these loci.
Women carrying more variant alleles would be at greater risk than those carrying fewer.
The output VCF file is the "master" (unfiltered) deposited set of variants (with a reference and one or more variant [non-reference] alleles specified at each locus), genotypes (with each individual at each locus either assigned to two [not necessarily distinct] alleles, or left uncalled and assigned to no alleles), and a large variety of embedded statistics.
If a sequencing or mapping error was the cause of variation, two or more variants were expected at a nucleotide position in a stack of reads, and the frequency of one of the variants was expected to be minor.
Dr. Kraft and Dr. Hunter say that a person's genetic risk of common diseases can be estimated only roughly at present but that estimates will improve as more variants are found.
Higher thresholds result in more accurate predictions at the cost of covering fewer variants; lower thresholds cover more variants while reducing accuracy.
Individuals from admixed American populations carry more heterozygous variants at constrained sites than individuals from European populations (p < 0.05), which in turn carry more than individuals from South East Asian populations (p < 0.05).
There was no significant effect of the more common variants (at positions 158588123 and 158587689).
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