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 mr1358 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
vg0224822504 sf0224816635 2 24822504 1.35E-10 4.52E-09
vg1123192315 sf1122726186 11 23192315 2.03E-08 3.59E-06
vg0717634270 sf0717633277 7 17634270 3.50E-08 NA
vg0317655545 sf0317654327 3 17655545 6.24E-08 NA
vg0801055392 sf0801054394 8 1055392 7.08E-06 4.67E-06
vg0205570340 sf0205570340 2 5570340 7.70E-06 NA
vg1218169215 sf1218140651 12 18169215 NA 4.66E-08
vg0500316114 sf0500316114 5 316114 NA 1.21E-06
vg0104000364 sf0103999364 1 4000364 NA 2.55E-06
vg0321827081 sf0321825591 3 21827081 NA 3.14E-06
vg1016891094 sf1016819866 10 16891094 NA 3.62E-06