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 mr1373 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
vg0424181194 sf0423996055 4 24181194 8.06E-09 7.37E-08
vg1103158490 sf1103154393 11 3158490 1.87E-08 2.02E-06
vg0122971893 sf0122970849 1 22971893 4.64E-08 2.45E-06
vg0717125545 sf0717124552 7 17125545 4.64E-08 3.54E-06
vg0420711795 sf0420539838 4 20711795 5.55E-08 4.00E-06
vg0709448532 sf0709447538 7 9448532 6.12E-08 1.41E-08
vg0420718113 sf0420546156 4 20718113 6.72E-08 1.74E-06
vg0921004343 sf0921003862 9 21004343 1.55E-07 6.78E-07
vg0421370963 sf0421199016 4 21370963 6.12E-07 2.64E-06
vg0817327549 sf0817324835 8 17327549 6.13E-07 1.42E-06
vg0623981969 sf0623980972 6 23981969 2.29E-06 3.95E-06
vg1104596684 sf1104592586 11 4596684 3.33E-06 3.32E-06
vg0200521736 sf0200521736 2 521736 3.77E-06 3.68E-06
vg0704732672 sf0704731673 7 4732672 4.76E-06 4.47E-06
vg0713442761 sf0713441768 7 13442761 5.32E-06 2.48E-06