Fig. 5
From: A pangenome analysis pipeline provides insights into functional gene identification in rice
GWAS of thousand grain weight in 413 international accessions. a Manhattan plots of SNP-GWAS and PAV-GWAS in chromosome 5 for the thousand grain weight trait. SNPs and PAVs were genotyped in the pangenome. b A zoomed view in 5.8 to 6.2 Mb of Manhattan plots of SNP-GWAS and PAV-GWAS in chromosome 5 for the thousand grain weight trait. c Haplotype analysis for the loci regulating the thousand grain traits. Hap1 contains the 370 bp deletion and without the 1212 bp and 950 bp deletions. Hap2 contains the 950bp deletion and without the 370bp deletion. Hap3 contains the 370 bp deletion as well as the 1212 bp deletions. PAV_Lemont_570 and PAV_Tumba_552 denoted the PAVs. The PAVs’ locations are shown in the pangenome by comparing them to the Nipponbare reference genome (MSU7.0). The red star indicates the position of the highest −log10(p-value) in PAV-GWAS