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 mr1829 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
vg0724505923 sf0724504929 7 24505923 7.78E-40 1.36E-38
vg0331001535 sf0330994422 3 31001535 7.39E-23 7.86E-10
vg0331247251 sf0331240136 3 31247251 1.76E-21 2.15E-15
vg0331280409 sf0331273294 3 31280409 4.88E-21 4.24E-16
vg0331305156 sf0331298041 3 31305156 7.18E-21 3.63E-15
vg0331256576 sf0331249461 3 31256576 5.81E-19 1.77E-12
vg1000401399 sf1000400399 10 401399 1.74E-17 2.80E-10
vg0400999452 sf0400995004 4 999452 4.11E-17 5.49E-12
vg1117591563 sf1117125420 11 17591563 1.93E-14 2.25E-11
vg0725312603 sf0725311609 7 25312603 4.20E-14 2.30E-13
vg0411929663 sf0411920374 4 11929663 5.02E-12 7.36E-08
vg0805636201 sf0805635204 8 5636201 1.87E-11 3.37E-08
vg0724532089 sf0724531095 7 24532089 2.52E-11 3.08E-23
vg0724609231 sf0724608237 7 24609231 4.96E-11 6.20E-08
vg1218122202 sf1218093638 12 18122202 6.84E-11 5.29E-08
vg0520507705 sf0520445176 5 20507705 1.95E-10 NA
vg0404387799 sf0404383403 4 4387799 3.26E-10 1.43E-08
vg0808289886 sf0808288890 8 8289886 1.42E-09 1.20E-07
vg0724381883 sf0724380889 7 24381883 4.70E-09 9.14E-12
vg0724510628 sf0724509634 7 24510628 5.86E-08 1.46E-12
vg0724473205 sf0724472211 7 24473205 1.62E-07 1.11E-13
vg1111856161 sf1111850478 11 11856161 2.04E-07 NA
vg0721876471 sf0721875478 7 21876471 4.55E-07 7.63E-09
vg0724294065 sf0724293071 7 24294065 NA 1.10E-12
vg0233123079 sf0233117210 2 33123079 NA 9.31E-10
vg1109484212 sf1109478789 11 9484212 NA 1.14E-08
vg1117593072 sf1117126929 11 17593072 NA 2.75E-08
vg0621137518 sf0621136521 6 21137518 NA 5.03E-08
vg0507092737 sf0507092679 5 7092737 NA 5.42E-07