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 mr1962 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
vg0222739831 sf0222733962 2 22739831 4.62E-56 3.41E-38
vg0224620629 sf0224614760 2 24620629 2.60E-18 2.92E-08
vg0223077967 sf0223072098 2 23077967 2.76E-17 2.28E-08
vg0120478712 sf0120477667 1 20478712 3.37E-17 NA
vg0223078170 sf0223072301 2 23078170 9.92E-17 4.64E-09
vg0223936690 sf0223930821 2 23936690 2.90E-15 NA
vg0224876512 sf0224870643 2 24876512 1.22E-14 3.78E-08
vg0222852279 sf0222846410 2 22852279 3.14E-14 9.33E-14
vg0223914026 sf0223908157 2 23914026 1.35E-12 3.33E-06
vg1007489401 sf1007505024 10 7489401 4.22E-12 NA
vg0224633236 sf0224627367 2 24633236 5.50E-12 5.36E-07
vg0223072760 sf0223066891 2 23072760 1.18E-10 3.77E-06
vg0722937821 sf0722936828 7 22937821 3.19E-10 NA
vg0223720122 sf0223714253 2 23720122 8.72E-10 2.04E-07
vg0222620162 sf0222614293 2 22620162 1.35E-09 5.98E-09
vg1216282260 sf1216279556 12 16282260 3.13E-09 NA
vg0223170147 sf0223164278 2 23170147 3.30E-09 2.64E-06
vg0222799001 sf0222793132 2 22799001 9.56E-09 4.68E-06
vg0222556850 sf0222550981 2 22556850 NA 5.95E-09
vg0414954715 sf0414945429 4 14954715 NA 2.03E-06
vg1215976459 sf1215973755 12 15976459 NA 2.78E-06
vg0209234819 sf0209234817 2 9234819 NA 3.27E-06
vg0504475516 sf0504475493 5 4475516 NA 3.42E-06
vg0402996309 sf0402991915 4 2996309 NA 3.67E-06