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 mr1216 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
vg0920070140 sf0920069659 9 20070140 5.98E-33 5.34E-22
vg0920039290 sf0920038809 9 20039290 8.77E-33 2.74E-22
vg0721197653 sf0721196660 7 21197653 1.30E-15 1.07E-08
vg0127445565 sf0127444521 1 27445565 3.76E-15 2.98E-08
vg0919789696 sf0919789215 9 19789696 1.90E-11 9.18E-08
vg0334365021 sf0334357891 3 34365021 1.15E-10 7.71E-06
vg0334371792 sf0334364662 3 34371792 3.47E-10 2.25E-06
vg0919873160 sf0919872679 9 19873160 8.02E-10 9.47E-07
vg0919910598 sf0919910117 9 19910598 1.30E-09 3.34E-08
vg0919618710 sf0919618300 9 19618710 9.70E-09 3.18E-06
vg0620524611 sf0620523614 6 20524611 1.21E-08 2.84E-07
vg0920313004 sf0920312523 9 20313004 4.57E-08 3.58E-07
vg0920271835 sf0920271354 9 20271835 5.47E-07 7.88E-07
vg1022610045 sf1022538519 10 22610045 9.14E-07 2.82E-06
vg0218153756 sf0218147887 2 18153756 NA 7.65E-07
vg0628632221 sf0628631223 6 28632221 NA 3.54E-06
vg0406063032 sf0406058471 4 6063032 NA 3.96E-06