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 mr1090 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
vg0610687764 sf0610686765 6 10687764 3.25E-17 2.02E-15
vg0610060451 sf0610059452 6 10060451 4.32E-14 9.64E-10
vg0610073622 sf0610072623 6 10073622 8.65E-14 6.73E-10
vg0610559877 sf0610558878 6 10559877 6.69E-12 1.52E-08
vg0403922278 sf0403917884 4 3922278 2.65E-11 2.68E-08
vg0616129303 sf0616128305 6 16129303 7.46E-10 3.26E-09
vg1126275743 sf1125804156 11 26275743 4.42E-09 NA
vg1004376825 sf1004393363 10 4376825 5.01E-09 2.39E-06
vg1001052701 sf1001051677 10 1052701 1.97E-08 4.67E-07
vg0610730892 sf0610729893 6 10730892 7.81E-08 3.17E-06
vg0612767306 sf0612766307 6 12767306 1.80E-07 3.12E-06
vg1123394093 sf1122927963 11 23394093 1.14E-06 4.26E-06
vg1209876216 sf1209873626 12 9876216 NA 2.88E-06
vg0311072594 sf0311071312 3 11072594 NA 6.01E-06