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 mr1403 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
vg1223872994 sf1223839447 12 23872994 1.91E-28 NA
vg0304934790 sf0304933792 3 4934790 4.14E-28 NA
vg1017936465 sf1017865237 10 17936465 5.86E-28 NA
vg0217654440 sf0217648570 2 17654440 7.48E-28 NA
vg0128353459 sf0128352415 1 28353459 9.03E-28 NA
vg0127208209 sf0127207165 1 27208209 1.18E-27 1.04E-07
vg0816544331 sf0816541617 8 16544331 NA 3.83E-08
vg1219761706 sf1219733176 12 19761706 NA 4.90E-08
vg1219751296 sf1219722766 12 19751296 NA 1.03E-07
vg1122935128 sf1122468999 11 22935128 NA 2.17E-07
vg0308974609 sf0308973547 3 8974609 NA 4.00E-07
vg1004515571 sf1004532109 10 4515571 NA 7.41E-07
vg1122958660 sf1122492531 11 22958660 NA 1.64E-06
vg1004272649 sf1004289187 10 4272649 NA 3.42E-06
vg0422820213 sf0422635096 4 22820213 NA 4.31E-06
vg1004519208 sf1004535746 10 4519208 NA 4.53E-06