Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1167 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0405539066 sf0405534507 4 5539066 5.41E-16 2.05E-09
vg0405387831 sf0405383272 4 5387831 2.48E-12 NA
vg0100780655 sf0100779655 1 780655 2.51E-10 NA
vg0402158888 sf0402154483 4 2158888 2.81E-10 NA
vg0528034305 sf0527971660 5 28034305 6.42E-10 NA
vg0421013459 sf0420841512 4 21013459 8.89E-10 1.96E-06
vg1121730637 sf1121264514 11 21730637 1.36E-08 NA
vg0805645208 sf0805644211 8 5645208 1.65E-08 1.02E-06
vg0816363117 sf0816360403 8 16363117 3.26E-08 1.05E-06
vg0817311608 sf0817308894 8 17311608 4.17E-08 4.98E-07
vg0517499780 sf0517439423 5 17499780 9.06E-08 NA
vg0909283736 sf0909282735 9 9283736 1.04E-07 3.05E-06
vg1112908740 sf1112445061 11 12908740 1.33E-07 2.21E-06
vg0817494161 sf0817491447 8 17494161 1.49E-07 3.36E-06
vg0701536585 sf0701535585 7 1536585 1.67E-07 NA
vg0408160817 sf0408156091 4 8160817 7.88E-07 1.56E-06
vg1110034908 sf1110029485 11 10034908 NA 4.82E-07
vg1205242086 sf1205241072 12 5242086 NA 1.83E-06
vg0408658440 sf0408653716 4 8658440 NA 3.02E-06
vg0404403925 sf0404399529 4 4403925 NA 3.20E-06
vg1015203758 sf1015132526 10 15203758 NA 3.36E-06
vg1209158100 sf1209155509 12 9158100 NA 3.57E-06
vg0209217731 sf0209217729 2 9217731 NA 4.76E-06
vg0722992016 sf0722991023 7 22992016 NA 7.89E-06