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 mr1093 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
vg0217033543 sf0217027673 2 17033543 6.56E-24 6.46E-19
vg0217612660 sf0217606790 2 17612660 1.55E-20 7.40E-13
vg0216721532 sf0216715662 2 16721532 1.77E-20 5.15E-13
vg0220342684 sf0220336816 2 20342684 1.52E-15 5.87E-09
vg0812023942 sf0812022947 8 12023942 4.64E-15 2.66E-10
vg1216424531 sf1216421824 12 16424531 4.73E-15 3.12E-06
vg0216662827 sf0216656957 2 16662827 5.07E-15 1.14E-09
vg1210817600 sf1210814966 12 10817600 9.02E-14 3.14E-07
vg0217387611 sf0217381741 2 17387611 1.19E-13 5.51E-08
vg0215898350 sf0215892480 2 15898350 1.73E-13 5.86E-07
vg0217737425 sf0217731555 2 17737425 5.51E-13 1.12E-08
vg0218852605 sf0218846736 2 18852605 3.82E-12 2.89E-07
vg0216134521 sf0216128651 2 16134521 5.43E-12 4.55E-08
vg0719727567 sf0719726574 7 19727567 6.07E-12 2.03E-06
vg0217797694 sf0217791825 2 17797694 2.13E-11 3.86E-07
vg0217679949 sf0217674079 2 17679949 5.46E-10 1.24E-06
vg0212179937 sf0212179933 2 12179937 6.69E-10 8.88E-07
vg1105771186 sf1105766938 11 5771186 1.06E-08 8.66E-07
vg0216646134 sf0216640264 2 16646134 2.09E-08 1.88E-06
vg0217039180 sf0217033310 2 17039180 2.32E-08 1.23E-07
vg0216093839 sf0216087969 2 16093839 3.02E-08 2.59E-06
vg0814543467 sf0814540753 8 14543467 NA 2.39E-06
vg0100239153 sf0100238153 1 239153 NA 2.69E-06