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 mr1652 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 4.47E-09 4.47E-09
vg0420711795 sf0420539838 4 20711795 4.65E-08 4.66E-08
vg0717125545 sf0717124552 7 17125545 3.33E-07 3.33E-07
vg0516508609 sf0516451091 5 16508609 5.80E-07 5.80E-07
vg0521872068 sf0521809510 5 21872068 8.28E-07 8.28E-07
vg0421384856 sf0421212909 4 21384856 1.07E-06 1.07E-06
vg0805826839 sf0805825842 8 5826839 1.41E-06 1.41E-06
vg0921004343 sf0921003862 9 21004343 1.66E-06 1.66E-06
vg0623981969 sf0623980972 6 23981969 2.07E-06 2.07E-06
vg0316786845 sf0316785719 3 16786845 2.20E-06 2.20E-06
vg1225484489 sf1225450884 12 25484489 2.48E-06 2.48E-06
vg0629854146 sf0629853148 6 29854146 2.64E-06 2.64E-06
vg0802999703 sf0802998706 8 2999703 3.12E-06 3.12E-06
vg0712843936 sf0712842943 7 12843936 3.17E-06 3.17E-06
vg0905437685 sf0905436685 9 5437685 4.42E-06 4.42E-06