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 mr1168 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
vg1000080974 sf1000079974 10 80974 1.42E-30 3.98E-10
vg0901035344 sf0901034344 9 1035344 1.01E-23 NA
vg1015182126 sf1015110894 10 15182126 4.11E-23 NA
vg0523997343 sf0523934763 5 23997343 6.80E-23 NA
vg0903984505 sf0903983505 9 3984505 9.74E-23 NA
vg1114423825 sf1113960142 11 14423825 6.69E-22 7.02E-08
vg0904000622 sf0903999622 9 4000622 8.40E-19 NA
vg0112438971 sf0112437945 1 12438971 1.10E-18 NA
vg1000207799 sf1000206799 10 207799 NA 1.31E-08
vg0700013911 sf0700012911 7 13911 NA 1.61E-08
vg0700053913 sf0700052913 7 53913 NA 2.60E-08
vg0700219361 sf0700218361 7 219361 NA 4.01E-07
vg0432523372 sf0432338264 4 32523372 NA 5.58E-07
vg0104860223 sf0104859223 1 4860223 NA 6.84E-07
vg0622507208 sf0622506211 6 22507208 NA 1.35E-06
vg1001622130 sf1001621107 10 1622130 NA 1.85E-06
vg0900043120 sf0900042120 9 43120 NA 2.20E-06
vg0127316647 sf0127315603 1 27316647 NA 3.20E-06