Allele coverage counts top Bayenv2.0 SNPs
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We provide here the Sync file of allele coverage counts for 2,978 SNPs for six populations of Lasallia pustulata that showed the highest score possible for Z in the Bayenv2.0 analysis.
Used populations and abbreviations:
1 => Population 1, 176 m a.s.l.
2 => Population 2, 297 m a.s.l.
3 => Population 3, 588 m a.s.l.
4 => Population 4, 842 m a.s.l.
5 => Population 5, 1,125 m a.s.l.
6 => Population 6, 1,303 m a.s.l.
Output of the Sync file (for format specification see Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436):
col1: scaffold number
col2: SNP position on scaffold
col3: reference character
col4: allele frequencies of population number 1
col5: allele frequencies of population number 2
coln: allele frequencies of population number n
The allele frequencies are in the format A:T:C:G:N:del, i.e: count of bases 'A', count of bases 'T', etc. , and deletion count in the end.
本研究提供了针对6个疱状石耳(Lasallia pustulata)种群的2978个单核苷酸多态性(Single Nucleotide Polymorphism,SNP)位点的等位基因覆盖计数Sync格式文件,这些种群在Bayenv2.0分析中获得了最高的Z值得分。
所用种群及其缩写如下:
1. 1号种群,海拔176米(m a.s.l.)
2. 2号种群,海拔297米(m a.s.l.)
3. 3号种群,海拔588米(m a.s.l.)
4. 4号种群,海拔842米(m a.s.l.)
5. 5号种群,海拔1125米(m a.s.l.)
6. 6号种群,海拔1303米(m a.s.l.)
Sync格式文件的输出列说明如下(格式规范详见Kofler等人发表于《生物信息学(Bioinformatics)》2011年第27卷第3435-3436页的研究论文《PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)》,即《PoPoolation2:利用混合DNA样本测序(Pool-Seq)鉴定种群间分化差异》):
第1列:支架序列(scaffold)编号
第2列:SNP在scaffold上的位置
第3列:参考碱基
第4列:1号种群的等位基因频率
第5列:2号种群的等位基因频率
……
第n列:n号种群的等位基因频率
等位基因频率采用A:T:C:G:N:del格式,即依次为碱基A、T、C、G、N的计数,以及末尾的缺失序列计数。
创建时间:
2017-03-03



