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 mr1925 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
vg0106686481 sf0106685481 1 6686481 6.91E-23 1.46E-18
vg0105661905 sf0105660905 1 5661905 1.05E-15 3.67E-08
vg0317879120 sf0317877902 3 17879120 9.01E-13 3.46E-07
vg0106684036 sf0106683036 1 6684036 1.12E-11 8.11E-10
vg0130455488 sf0130454444 1 30455488 1.66E-10 NA
vg0107015284 sf0107014284 1 7015284 7.92E-09 7.77E-10
vg1222936918 sf1222903377 12 22936918 8.62E-08 NA
vg0125391488 sf0125390444 1 25391488 6.77E-06 NA
vg0604059961 sf0604058962 6 4059961 NA 4.22E-07
vg0323946857 sf0323945031 3 23946857 NA 6.63E-07
vg0901587632 sf0901586632 9 1587632 NA 9.96E-07
vg0317498077 sf0317496859 3 17498077 NA 1.26E-06