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 mr1913 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
vg0406356417 sf0406351857 4 6356417 5.76E-28 1.68E-16
vg0406145439 sf0406140879 4 6145439 8.45E-28 1.97E-16
vg0406661532 sf0406656980 4 6661532 1.05E-20 3.50E-09
vg0406865389 sf0406860834 4 6865389 6.43E-16 3.07E-07
vg1122924753 sf1122458624 11 22924753 2.68E-15 1.51E-08
vg1016330569 sf1016259345 10 16330569 1.04E-14 NA
vg0724012275 sf0724011281 7 24012275 2.29E-13 2.04E-07
vg1004482207 sf1004498745 10 4482207 5.60E-13 1.28E-08
vg0801674326 sf0801673328 8 1674326 9.69E-11 7.18E-07
vg1105201111 sf1105196922 11 5201111 1.12E-10 7.00E-08
vg1122629035 sf1122162906 11 22629035 5.50E-10 1.60E-06
vg0912864929 sf0912863928 9 12864929 1.55E-09 2.83E-06
vg0703570919 sf0703569920 7 3570919 1.22E-07 6.10E-07
vg0518836423 sf0518773907 5 18836423 2.27E-07 4.02E-06
vg1121623117 sf1121156994 11 21623117 2.65E-07 7.53E-08
vg0224803813 sf0224797944 2 24803813 4.75E-06 4.49E-06
vg0430673937 sf0430488812 4 30673937 9.14E-06 1.43E-06
vg0105551046 sf0105550046 1 5551046 NA 4.55E-06