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PyBSASeq: a simple and effective algorithm for bulked segregant ...
Mar 6, 2020 · The current SNP index method and G-statistic method for BSA-Seq data analysis require relatively high sequencing coverage to detect significant single nucleotide polymorphism (SNP)-trait associations, which leads to high sequencing cost.
BSA分析算法中的ED算法和SNP-index有什么区别？ - 组学大 ...
Aug 2, 2019 · SNP-index方法是一种通过计算混池间的基因型频率差异进行标记关联分析的方法，主要是寻找混池之间基因型频率的显著差异，用Δ(SNP-index)统计。 Marker与性状关联度越强，Δ (SNP-index)越接近于 1。 计算方法简述如下： 通过在基因组上选择一定大小的窗口，如100Kb，通过滑窗法在全基因组水平内对窗口内包含的SNP进行计算，得到两个极端混池Δ (SNP_index)的值，然后对在同一条染色体上的SNP标记的Δ (SNP_index)进行LOESS回归拟 …
什么是“SNP-index”？| 群体遗传专题_进行 - 搜狐
May 18, 2020 · SNP-index这个词，作为BSA的最常用的核心算法，给出的是BSA类项目最重要的QTL定位结果。 SNP-index通过结果的可视化，可以非常直观地看出BSA定位得到的QTL在基因组上的位置。
GWAS terminology "Tag" vs "Lead" vs "Index" SNP
May 25, 2018 · Lead SNP = Index SNP - the SNP assigned the highest association significance after we've run association analysis for all the imputed SNP. The other SNPs in high LD with the lead SNP will form the associated locus.
Genome sequencing reveals agronomically important loci in …
Jan 22, 2012 · For Hit1917-pl1, a pale green leaf mutant, we examined SNPs with SNP index of 1 in detail. Of seven SNPs with SNP index of 1, two corresponded to exons of protein-coding genes.
QTLseqr: An R Package for Bulk Segregant Analysis with Next
Jul 1, 2018 · Takagi and colleagues define the ∆ (SNP-index) for each SNP as the difference of the low value bulk SNP-index from the high value bulk SNP-index. They suggest averaging and plotting ∆ (SNP-indices) over a sliding window.
Topic 9 - SNP Filtering and Analysis · Bioinformatics for …
In this tutorial we’re going to use SNPs called with GATK to analyse patterns of population structure in the Chinook genome and conduct a GWAS. The specific data that you apply to analyses is obviously important (garbage in, garbage out). We’re going to play around with some SNP filters to test their effects on downstream analyses with our ...
ISOGG - SNPedia
Oct 7, 2014 · The SNP index 2014 lists the SNPs which are either on the ISOGG Y Haplotree, or that are or have been under active investigation and consideration for addition to the ISOGG Y Haplogroup tree. The SNPs in the ISOGG SNP list 2014 are less than 10% of the currently known Chromosome Y SNPs.