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 mr1770 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
vg0335383525 sf0335376394 3 35383525 6.26E-07 6.26E-07
vg1021671439 sf1021599917 10 21671439 7.48E-07 7.49E-07
vg0700645458 sf0700644458 7 645458 8.88E-07 8.88E-07
vg0421072597 sf0420900652 4 21072597 9.02E-07 9.02E-07
vg0334267558 sf0334260428 3 34267558 1.20E-06 1.20E-06
vg0406869281 sf0406864726 4 6869281 1.23E-06 1.23E-06
vg0307862708 sf0307861646 3 7862708 1.81E-06 1.81E-06
vg1100024654 sf1100023654 11 24654 1.84E-06 1.84E-06
vg0208038424 sf0208038423 2 8038424 2.07E-06 2.07E-06
vg1012383116 sf1012311931 10 12383116 2.40E-06 2.40E-06
vg1217860963 sf1217832397 12 17860963 2.75E-06 2.75E-06
vg0141980593 sf0141979550 1 41980593 2.99E-06 2.99E-06
vg0913502387 sf0913501386 9 13502387 3.08E-06 3.08E-06
vg0600529931 sf0600528932 6 529931 3.16E-06 3.16E-06
vg1120996498 sf1120530377 11 20996498 3.47E-06 3.47E-06
vg0207103437 sf0207103437 2 7103437 4.09E-06 4.09E-06
vg0504429178 sf0504429155 5 4429178 4.38E-06 4.38E-06
vg0226040711 sf0226034842 2 26040711 4.58E-06 4.58E-06
vg1121358068 sf1120891945 11 21358068 4.59E-06 4.59E-06
vg0142041116 sf0142040073 1 42041116 4.90E-06 4.90E-06