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 mr1993 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
vg0417352590 sf0417180633 4 17352590 1.29E-24 8.38E-12
vg0417244171 sf0417072212 4 17244171 3.88E-24 3.84E-14
vg0718541494 sf0718540501 7 18541494 1.20E-18 2.63E-08
vg0718516017 sf0718515024 7 18516017 2.01E-18 2.24E-08
vg0612029827 sf0612028828 6 12029827 2.83E-18 1.09E-06
vg0707076224 sf0707075229 7 7076224 2.95E-18 NA
vg0707065048 sf0707064053 7 7065048 3.83E-18 2.06E-07
vg0427084460 sf0426899332 4 27084460 4.68E-18 NA
vg0519939017 sf0519876493 5 19939017 6.07E-17 1.63E-07
vg0410354028 sf0410344727 4 10354028 4.51E-16 1.42E-08
vg0508890508 sf0508890436 5 8890508 9.66E-16 3.27E-06
vg0817173341 sf0817170627 8 17173341 2.91E-15 3.37E-08
vg0403055424 sf0403051028 4 3055424 6.57E-15 2.36E-08
vg0211588654 sf0211588650 2 11588654 1.20E-14 7.89E-07
vg0421592157 sf0421420207 4 21592157 1.35E-14 7.78E-07
vg0406753488 sf0406748934 4 6753488 2.01E-14 1.22E-06
vg0721234062 sf0721233069 7 21234062 8.57E-13 1.34E-07
vg0715882829 sf0715881836 7 15882829 1.12E-11 3.51E-06
vg0419225907 sf0419053945 4 19225907 NA 1.68E-07
vg0142429070 sf0142428026 1 42429070 NA 8.58E-07
vg0227957829 sf0227951960 2 27957829 NA 8.71E-07
vg0718523888 sf0718522895 7 18523888 NA 1.87E-06
vg0805968808 sf0805967811 8 5968808 NA 2.88E-06
vg0917957186 sf0917956185 9 17957186 NA 3.21E-06
vg1216930812 sf1216924766 12 16930812 NA 3.47E-06
vg0209944299 sf0209944297 2 9944299 NA 7.41E-06