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 mr1095 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
vg0222739831 sf0222733962 2 22739831 4.44E-45 3.27E-35
vg0224284988 sf0224279119 2 24284988 8.55E-12 1.29E-06
vg0224678258 sf0224672389 2 24678258 3.86E-11 2.04E-08
vg0223641214 sf0223635345 2 23641214 8.59E-11 3.19E-08
vg0223053830 sf0223047961 2 23053830 1.35E-10 NA
vg0224664402 sf0224658533 2 24664402 6.36E-10 1.21E-09
vg0222879623 sf0222873754 2 22879623 1.27E-09 1.55E-09
vg0120651124 sf0120650079 1 20651124 1.12E-08 4.26E-06
vg0224788519 sf0224782650 2 24788519 4.58E-08 9.68E-07
vg0222624829 sf0222618960 2 22624829 4.62E-08 3.85E-09
vg0219769577 sf0219763709 2 19769577 9.97E-08 NA
vg1112606104 sf1112142307 11 12606104 2.38E-07 2.77E-06
vg0224797317 sf0224791448 2 24797317 6.78E-07 3.41E-06
vg0221953494 sf0221947625 2 21953494 9.19E-07 3.10E-06
vg0205189046 sf0205189043 2 5189046 2.64E-06 1.35E-06
vg0224626347 sf0224620478 2 24626347 NA 7.29E-07
vg0713058371 sf0713057378 7 13058371 NA 1.80E-06
vg0321930604 sf0321929113 3 21930604 NA 3.62E-06
vg0409867510 sf0409858208 4 9867510 NA 4.30E-06
vg0500201539 sf0500201539 5 201539 NA 4.97E-06