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 mr1980 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
vg1013533412 sf1013462182 10 13533412 5.32E-90 1.25E-46
vg1007654340 sf1007669949 10 7654340 5.03E-38 NA
vg0106891421 sf0106890421 1 6891421 6.06E-37 NA
vg0821189139 sf0821186426 8 21189139 1.23E-36 NA
vg0800348884 sf0800347884 8 348884 4.74E-36 NA
vg1013528182 sf1013456952 10 13528182 NA 5.81E-28
vg1013528778 sf1013457548 10 13528778 NA 1.60E-15
vg1013277454 sf1013206223 10 13277454 NA 3.49E-13
vg1013542818 sf1013471588 10 13542818 NA 4.07E-10
vg1013130507 sf1013059278 10 13130507 NA 3.30E-09
vg0817676420 sf0817673707 8 17676420 NA 1.05E-08
vg1013769802 sf1013698571 10 13769802 NA 2.35E-08
vg1013500622 sf1013429392 10 13500622 NA 4.93E-08
vg1013800146 sf1013728915 10 13800146 NA 1.53E-07
vg0817661668 sf0817658955 8 17661668 NA 1.78E-07
vg0817567492 sf0817564778 8 17567492 NA 6.38E-07
vg1119520666 sf1119054354 11 19520666 NA 2.12E-06
vg0718328688 sf0718327695 7 18328688 NA 2.50E-06
vg0302039011 sf0302038007 3 2039011 NA 2.50E-06
vg1013651285 sf1013580054 10 13651285 NA 2.50E-06
vg0301869529 sf0301868525 3 1869529 NA 3.91E-06