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 mr1402 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
vg0406420586 sf0406416026 4 6420586 8.19E-85 9.35E-16
vg0406728056 sf0406723502 4 6728056 4.59E-74 1.53E-08
vg0411344776 sf0411335479 4 11344776 3.35E-70 NA
vg0305432083 sf0305431083 3 5432083 4.19E-70 NA
vg0917981166 sf0917980165 9 17981166 1.22E-69 NA
vg0504661489 sf0504661466 5 4661489 6.05E-69 NA
vg0222726563 sf0222720694 2 22726563 NA 1.98E-08
vg0222719698 sf0222713829 2 22719698 NA 3.94E-08
vg1209893179 sf1209890589 12 9893179 NA 8.38E-08
vg0707650970 sf0707649975 7 7650970 NA 2.77E-07
vg0206270004 sf0206270004 2 6270004 NA 1.49E-06
vg0406521772 sf0406517215 4 6521772 NA 2.06E-06
vg0406523938 sf0406519381 4 6523938 NA 2.51E-06
vg0819136160 sf0819133447 8 19136160 NA 2.55E-06
vg0222743387 sf0222737518 2 22743387 NA 3.03E-06
vg0805469573 sf0805468576 8 5469573 NA 4.24E-06
vg1010229159 sf1010157980 10 10229159 NA 4.26E-06
vg0427006874 sf0426821747 4 27006874 NA 4.62E-06
vg0904010040 sf0904009040 9 4010040 NA 5.07E-06