Fig. 6
From: A pangenome analysis pipeline provides insights into functional gene identification in rice
GWAS of plant height in 413 international rice accessions. a Manhattan plot of SNP- and PAV-GWAS in chromosome 8 for plant height. SNPs and PAVs were genotyped using the pangenome. The most significant hit was detected around the 10-Mb region. Two regions (PAV markers at 3,117,040 and 4,761,060 bp) also surpass the significance threshold of 5 −log(P). b A zoomed view of the 3.5- to 6-Mb region of the Manhattan plot of SNP-GWAS and PAV-GWAS in chromosome 8 for plant height. c, d Box plot of plant height and relative expressions level of Loc_Os08g07400 in 10 accessions contains (present, blue points) and 10 accessions without (absent, red points) the 13-kb insertion. The p-values were determined using two-tailed Student’s t tests. The middle bars represent the median, and the bottom and top of each box represent the 25th and 75th percentiles. The whiskers extend to 1.5 times the interquartile range