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 mr1522 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
vg0308448402 sf0308447340 3 8448402 1.21E-11 3.38E-06
vg0719389690 sf0719388697 7 19389690 3.32E-10 NA
vg0207793492 sf0207793491 2 7793492 3.67E-10 NA
vg0307955579 sf0307954517 3 7955579 1.07E-09 NA
vg0420712708 sf0420540751 4 20712708 1.85E-09 NA
vg1003008433 sf1003007410 10 3008433 1.55E-08 4.75E-07
vg1126875179 sf1126403566 11 26875179 3.46E-07 8.37E-07
vg0609042750 sf0609041751 6 9042750 6.92E-07 NA
vg1015264303 sf1015193071 10 15264303 4.88E-06 NA
vg1112963070 sf1112499391 11 12963070 NA 2.84E-06
vg0424904137 sf0424718998 4 24904137 NA 4.29E-06