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 mr1148 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
vg0222741535 sf0222735666 2 22741535 7.51E-25 1.98E-18
vg0222726032 sf0222720163 2 22726032 4.23E-24 1.50E-18
vg0223077967 sf0223072098 2 23077967 4.61E-13 4.16E-09
vg0321809218 sf0321807728 3 21809218 6.84E-11 NA
vg0222846586 sf0222840717 2 22846586 9.01E-11 3.26E-06
vg0224621250 sf0224615381 2 24621250 1.10E-10 NA
vg0224868229 sf0224862360 2 24868229 1.01E-09 2.45E-06
vg0224260935 sf0224255066 2 24260935 2.78E-08 3.53E-06
vg0611413430 sf0611412431 6 11413430 6.07E-08 1.41E-06
vg0222858963 sf0222853094 2 22858963 1.29E-07 9.53E-07
vg1126694376 sf1126222763 11 26694376 2.54E-07 3.92E-06
vg1121561200 sf1121095077 11 21561200 2.05E-06 4.76E-06
vg0222556989 sf0222551120 2 22556989 NA 2.89E-06
vg1217811728 sf1217783162 12 17811728 NA 4.51E-06