The single nucleotide polymorphism (SNP) calling are based on a total of 89 genome resequencing of Ananas accessions with the pineapple F153 as reference genome by using BWA (Version: 0.7.12-r1039) with the default parameters. The mapping files were tranfer into the BAM format used SAMtools(Vesion:1.3) and the duplicated reads were filter by the Picard package.The SNP were detect by using the Genome Analysis Toolkit (GATK, version 3.7-0-gcfedb67) . The neighbor-joining tree was constructed using SNPhylo software with the bootstrap 100. Finally, we identified 7,252,423 SNPs and 923,469 indels in the pineapple genome. We implemented phylogenetic analysis of 89 accessions using MEGA7.0, the results are as follows.

Note: You may click here to download and known the varieties of information of every accession. you may observe the visualization of the SNP loci by JBrowse (Click on each mutation sites in JBrowse to check detail corresponding variability information of each accession).