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 mr1698 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
vg1121744807 sf1121278684 11 21744807 3.20E-09 7.62E-07
vg1121842515 sf1121376392 11 21842515 3.38E-09 7.68E-07
vg1003302040 sf1003301017 10 3302040 1.16E-08 7.27E-08
vg0402942194 sf0402937800 4 2942194 2.65E-08 2.65E-08
vg0402068004 sf0402063599 4 2068004 4.45E-08 3.65E-06
vg1003302932 sf1003301909 10 3302932 1.19E-07 7.74E-07
vg0128629137 sf0128628092 1 28629137 2.30E-07 1.22E-07
vg0710603879 sf0710602885 7 10603879 8.25E-07 5.85E-07
vg0404607386 sf0404602989 4 4607386 1.13E-06 3.38E-06
vg0608286187 sf0608285188 6 8286187 NA 1.27E-06
vg1206253234 sf1206252124 12 6253234 NA 4.02E-06
vg0519136766 sf0519074250 5 19136766 NA 4.13E-06