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Genome Variation typically means variation of individual genomes within = a species. Variation between species is the realm of phylogenetics and/or c= omparative genomics.
Variants commonly detected by NGS consist of:
Yesterday we looked at the generalized w= orkflow for finding variants with NGS. Here is an image displaying SNPs= and indels in IGV. BP 615 is a heterozygote WT/MT (0/1); BP 624 is a homoz= ygous SNP; BP 643-649 is a heterozygous 6 bp deletion; BP 674 is a heterozy= gous 3 bp deletion.
Would you believe me if I told you this data were from a normal individu= al mammalian genome?
Variant analysis is almost always comparative, whether comparing variati= on rates, tracking traits, or looking for causal mutations. These compariso= ns can start with tools to analyze BAM files to identify putative variants = (the Variant Caller) and then continue into more detailed annotations (the = Variant Annotator).
We will introduce you to all these stages; keep in mind that this course= makes no assumption about the genome you're analyzing - it could be: