Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2013 May;23(5):833–842. doi: 10.1101/gr.146084.112

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 2013, Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.

PMC Copyright notice

Figure 3. — SNP statistics for sites discovered in 1000G PHASE1 with SNPTools. SNP sites were discovered using the variance ratio statistic. The unfiltered autosomal site list was composed of 34,656,295 candidate SNP sites, with an average Ti/Tv ratio of 2.11. SNPs were filtered using four criteria (Supplemental Material) to produce a final list of 32,737,954 SNPs with a Ti/Tv ratio of 2.15. (A) We found that 78.3% of the ∼32.7 million SNP were novel when evaluated with dbSNP 129. These novel sites had a Ti/Tv ratio of 2.15, which was comparable to the Ti/Tv of known sites, 2.17. (B) The site frequency spectrum of our discovered SNPs reveals that most novel SNPs were rare with MAF < 0.5%. (C) We provide discovery statistics for Chr20 and for the whole genome. Known SNPs are defined as being present in dbSNP129. SNPTools had a low false-discovery rate of 1284 sites out of 99,817 monomorphic OMNI sites.