Title:
Population genomic footprints of selection and associations with climate in
natural populations of Arabidopsis halleri from the Alps
We provide here the SNP file of five populations investigated in a population resequencing study of Arabidopsis halleri (Fischer et al. 2013).
Within the Aha_09_11_19_21_31_rc file you can find the 2,091,957 SNPs as well
as some small insertions and deletions in in the format of PoPoolation2 (Kofler et
al. 2011). The paired-end reads have been mapped against the five chromosomes
of Arabidopsis thaliana (TAIR10) using BWA (Li & Durbin 2009).
Used populations and abbreviations (for detailed coordinates see Fischer et al.
2013):
1 => Aha_09
2 => Aha_11
3 => Aha_19
4 => Aha_21
5 => Aha_31
OUTPUT of the Aha_09_11_19_21_31_rc file:
##chr pos
rc
allele_count
allele_states
major_alleles(maa)
minor_alleles(mia)
maa_5 mia_1 mia_2 mia_3 mia_4 mia_5
Chr1
2194 N
2
C/T
0
pop
49/49 27/27 51/51 7/75 0/45 0/49
deletion_sum
snp_type
maa_1 maa_2 maa_3 maa_4
CCCCC TNNNN 68/75 45/45
0/27 0/51
col1: reference chromosome (contig)
col2: referenced position
col3: reference character
col4: number of alleles found in all populations
col5: allele characters in all populations (sorted by counts in all populations)
col6: sum of deletions in all populations (should be zero, if not the position may not be reliable)
col7: SNP type: [pop, rc, rc|pop]; pop.. a SNP within or between the populations; rc. a SNP
between the reference sequence character and the consensus of at least one population;
rc|pop..both
col8: most frequent allele in all populations [12345..]
col9: second most frequent allele in all populations [12345..]
col10 - col9+n: frequencies of the most frequent allele (major) in the form "allelecount/coverage"
col10+n - col9+2n: frequencies of the second most frequent allele (minor) in the form "allelecount/coverage"
References
Kofler R, Pandey RV, Schlötterer C (2011) PoPoolation2: identifying differentiation
between populations using sequencing of pooled DNA samples (Pool-Seq).
Bioinformatics 27, 3435-3436.
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler
transform. Bioinformatics 25, 1754-1760.