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We tallied 44,529 splice variants seen at least once across ~12,000 sequenced samples. Among these splice variants, the majority were seen only once (27,265). Of the remaining variants (17,264), a total of 12,662 were seen in at least 2 datasets and are considered as candidates for inclusion in exome SNP arrays. The transition transversion ratio of this class of variants was 2.13 for all variants and 2.94 for variants that met criteria for inclusion in these arrays (being seen 2 or more times and in 2 or more studies).
We tallied 44,529 splice variants seen at least once across ~12,000 sequenced samples. Among these splice variants, the majority were seen only once (27,265). Of the remaining variants (17,264), a total of 12,662 were seen in at least 2 datasets and are considered as candidates for inclusion in exome SNP arrays. The transition transversion ratio of this class of variants was 2.13 for all variants and 2.94 for variants that met criteria for inclusion in these arrays (being seen 2 or more times and in 2 or more studies).
We estimate the candidate list of variants includes 94-95% of the stop altering variants detected in an average genome through exome sequencing.
We estimate the candidate list of variants includes 94-95% of the splice altering variants detected in an average genome through exome sequencing.
== Stop Altering Variants ==
== Stop Altering Variants ==
We tallied 30,508 stop altering variants (stop gains or losses) seen at least once across ~12,000 sequenced samples. Among the non-synonymous variants, the majority were seen only once (20,391). Of the remaining variants (10,117), a total of 7,029 were seen in at least 2 datasets and are considered as candidates for inclusion in exome SNP arrays. The transition transversion ratio of this class of variants was XXX for variants in dbSNP 132 and XXX for non dbSNP variants.
We tallied 31,003 stop altering variants (stop gains or losses) seen at least once across ~12,000 sequenced samples. Among the non-synonymous variants, the majority were seen only once (20,637). Of the remaining variants (10,366), a total of 7,137 were seen in at least 2 datasets and are considered as candidates for inclusion in exome SNP arrays. The transition transversion ratio of this class of variants was 1.68 for all variants and 2.29 for variants that met criteria for inclusion in these arrays (being seen 2 or more times and in 2 or more studies).
We estimate the candidate list of variants includes 94-95% of the stop altering variants detected in an average genome through exome sequencing.
== List of Candidate Variants ==
The full list of candidate variants is available by [ftp://share.sph.umich.edu/exomeChip/ProposedContent/codingContent anonymous ftp]. Each variant is annotated with the number of times it was seen, the number of studies in which it was seen, and its impact on protein sequence.
= Additional Content =
= Additional Content =
