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 mr1067 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
vg0223446523 sf0223440654 2 23446523 5.12E-08 5.12E-08
vg0819654266 sf0819651553 8 19654266 2.46E-07 2.46E-07
vg0224357857 sf0224351988 2 24357857 2.61E-07 2.61E-07
vg0235178053 sf0235172184 2 35178053 3.92E-07 3.92E-07
vg0321972978 sf0321971485 3 21972978 4.06E-07 4.06E-07
vg0823805704 sf0823802990 8 23805704 5.49E-07 5.49E-07
vg1102942974 sf1102938878 11 2942974 6.47E-07 6.47E-07
vg0724265685 sf0724264691 7 24265685 7.29E-07 7.29E-07
vg0807357132 sf0807356137 8 7357132 8.22E-07 8.22E-07
vg1215101661 sf1215098998 12 15101661 1.00E-06 1.00E-06
vg0620772509 sf0620771512 6 20772509 1.04E-06 1.04E-06
vg0205851172 sf0205851172 2 5851172 1.32E-06 1.32E-06
vg0202318103 sf0202318101 2 2318103 1.49E-06 1.48E-06
vg1017759585 sf1017688358 10 17759585 1.50E-06 1.50E-06
vg0207636002 sf0207636002 2 7636002 2.13E-06 2.13E-06
vg1106662965 sf1106658718 11 6662965 2.18E-06 2.18E-06
vg0141387129 sf0141386086 1 41387129 2.42E-06 2.42E-06
vg0134320161 sf0134319118 1 34320161 2.48E-06 2.48E-06
vg1222668845 sf1222635284 12 22668845 2.57E-06 2.57E-06
vg0330666534 sf0330659421 3 30666534 2.71E-06 2.71E-06