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 mr1203 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
vg0406465683 sf0406461126 4 6465683 3.45E-29 6.57E-21
vg0817327521 sf0817324807 8 17327521 5.72E-12 1.43E-07
vg1016565386 sf1016494159 10 16565386 3.64E-11 NA
vg1017940079 sf1017868851 10 17940079 1.25E-10 2.74E-06
vg1016503788 sf1016432561 10 16503788 3.14E-10 NA
vg0912864929 sf0912863928 9 12864929 3.58E-10 1.39E-06
vg0807357132 sf0807356137 8 7357132 4.78E-10 1.02E-06
vg0912152486 sf0912151485 9 12152486 4.83E-09 5.58E-07
vg0622629240 sf0622628243 6 22629240 2.33E-08 3.03E-07
vg0406056639 sf0406052078 4 6056639 2.57E-08 1.55E-08
vg0912757627 sf0912756626 9 12757627 5.02E-08 2.10E-07
vg0900339005 sf0900338005 9 339005 7.59E-08 2.51E-07
vg1116610872 sf1116145750 11 16610872 2.25E-07 6.00E-07
vg1209797289 sf1209794699 12 9797289 3.29E-07 3.97E-06
vg1216561117 sf1216558410 12 16561117 8.61E-07 8.02E-07
vg1216438393 sf1216435686 12 16438393 8.92E-07 4.69E-06
vg0710830865 sf0710829871 7 10830865 1.34E-06 1.75E-06
vg0509256609 sf0509256538 5 9256609 3.66E-06 3.29E-06
vg0417549349 sf0417377391 4 17549349 6.14E-06 9.24E-07