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 mr1335 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
vg0524382156 sf0524319577 5 24382156 9.00E-10 9.00E-10
vg0520492483 sf0520429954 5 20492483 1.86E-08 1.86E-08
vg0211327855 sf0211327852 2 11327855 5.15E-08 5.15E-08
vg0410246763 sf0410237460 4 10246763 8.80E-08 8.80E-08
vg0709880588 sf0709879594 7 9880588 1.35E-07 1.35E-07
vg0235474703 sf0235468834 2 35474703 1.37E-07 1.37E-07
vg1211085119 sf1211082485 12 11085119 2.61E-07 2.61E-07
vg0327684087 sf0327677140 3 27684087 2.77E-07 2.77E-07
vg0228484792 sf0228478923 2 28484792 2.96E-07 2.96E-07
vg1205661778 sf1205660760 12 5661778 3.16E-07 3.16E-07
vg1015774842 sf1015703612 10 15774842 3.64E-07 3.64E-07
vg0421123757 sf0420951809 4 21123757 5.06E-07 5.06E-07
vg0914999957 sf0914998956 9 14999957 5.62E-07 5.62E-07
vg1117878765 sf1117412622 11 17878765 5.95E-07 5.95E-07
vg0401663988 sf0401659537 4 1663988 6.68E-07 6.68E-07
vg1004715734 sf1004732271 10 4715734 9.19E-07 9.19E-07
vg0227378385 sf0227372516 2 27378385 9.20E-07 9.20E-07
vg1215653075 sf1215650372 12 15653075 9.78E-07 9.78E-07
vg0905565379 sf0905564379 9 5565379 1.04E-06 1.04E-06
vg1213728830 sf1213726168 12 13728830 1.09E-06 1.09E-06