Useage & attention
select one chromosome from 26 chomosomes (A01-A13,D01-D13) and the location (from start to end). Scaffolds were not included in this.
you can filter SNPs/InDels loci based on the variant type, annotation, population and allele frequency.
All the Varition results was identified by fastqc(QC),sickle(Trim),
bwa(Map to reference TM-1_V2.1), samtools,
Sambamba/picard(Duplicates Marking),bctools/GATK(variation calling).