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Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP/indel calling and alignment.
The calculation of prior probabilities depends on available data from the genome being studied, and the type of analysis being performed. For studies where good reference data containing frequencies of known mutations is available (for example, in studying human genome data), these known frequencies of genotypes in the population can be used to estimate priors.
Single nucleotide polymorphism annotation (SNP annotation) is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query.
Reparse Point (L): The file or directory has an associated re-parse point, or is a symbolic link. Offline (O): The file data is physically moved to offline storage (Remote Storage). Sparse (P): The file is a sparse file, i.e., its contents are partially empty and non-contiguous. Temporary (T): The file is used for temporary storage.
The upper DNA molecule differs from the lower DNA molecule at a single base-pair location (a G/A polymorphism) In genetics and bioinformatics, a single-nucleotide polymorphism (SNP / s n ɪ p /; plural SNPs / s n ɪ p s /) is a germline substitution of a single nucleotide at a specific position in the genome.
File descriptors for a single process, file table and inode table. Note that multiple file descriptors can refer to the same file table entry (e.g., as a result of the dup system call [3]: 104 ) and that multiple file table entries can in turn refer to the same inode (if it has been opened multiple times; the table is still simplified because it represents inodes by file names, even though an ...
1. Introduce the reference of a SNP of interest, as an example: rs429358, in a database (dbSNP or other). 2. Find MAF/MinorAlleleCount link. MAF/MinorAlleleCount: C=0.1506/754 (1000 Genomes, where number of genomes sampled = N = 2504); [4] where C is the minor allele for that particular locus; 0.1506 is the frequency of the C allele (MAF), i.e. 15% within the 1000 Genomes database; and 754 is ...
Slider is an application for the Illumina Sequence Analyzer output that uses the "probability" files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Yes Yes No No [53] [54] 2009-2010 SOAP, SOAP2, SOAP3, SOAP3-dp SOAP: robust with a small (1-3) number of gaps and mismatches.