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 mr1110 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
vg0610487064 sf0610486065 6 10487064 6.95E-11 2.98E-09
vg0610648813 sf0610647814 6 10648813 8.66E-11 2.76E-09
vg0403922278 sf0403917884 4 3922278 5.09E-09 4.53E-07
vg1009948618 sf1009877439 10 9948618 3.21E-08 NA
vg1210113739 sf1210111150 12 10113739 6.07E-08 3.44E-07
vg1004750280 sf1004766817 10 4750280 7.14E-08 NA
vg1217835762 sf1217807196 12 17835762 1.02E-07 2.20E-06
vg0626882641 sf0626881644 6 26882641 6.09E-07 9.71E-07
vg1206753482 sf1206752372 12 6753482 1.29E-06 3.36E-06
vg1218885208 sf1218856643 12 18885208 3.09E-06 NA
vg1203702115 sf1203701114 12 3702115 6.41E-06 4.55E-07
vg0809578434 sf0809577438 8 9578434 7.51E-06 3.41E-06