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 mr1245 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
vg0709448532 sf0709447538 7 9448532 5.90E-09 5.56E-09
vg0717125545 sf0717124552 7 17125545 7.37E-08 2.33E-06
vg0420711795 sf0420539838 4 20711795 2.28E-07 3.42E-06
vg0424181194 sf0423996055 4 24181194 3.43E-07 1.33E-06
vg1103158490 sf1103154393 11 3158490 4.61E-07 3.85E-06
vg0521872068 sf0521809510 5 21872068 6.00E-07 1.09E-06
vg0714179494 sf0714178501 7 14179494 7.24E-07 7.38E-07
vg0623981969 sf0623980972 6 23981969 1.20E-06 2.21E-06
vg0921004343 sf0921003862 9 21004343 1.39E-06 3.04E-06
vg0629854146 sf0629853148 6 29854146 1.60E-06 1.73E-06
vg0802999703 sf0802998706 8 2999703 2.40E-06 4.86E-06
vg1000501145 sf1000500121 10 501145 8.96E-06 3.79E-06