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 mr1697 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
vg0505514888 sf0505514826 5 5514888 2.72E-13 1.12E-08
vg0505628393 sf0505628331 5 5628393 7.58E-13 4.63E-14
vg0505633755 sf0505633693 5 5633755 1.18E-12 1.39E-14
vg0202086695 sf0202086695 2 2086695 1.23E-10 3.91E-07
vg0202081722 sf0202081722 2 2081722 1.50E-10 3.47E-07
vg1216052299 sf1216049595 12 16052299 8.19E-10 5.33E-06
vg0505490599 sf0505490577 5 5490599 9.05E-10 8.82E-08
vg0505864665 sf0505864603 5 5864665 1.53E-09 9.35E-08
vg0611477699 sf0611476700 6 11477699 8.34E-09 2.99E-06
vg0611005857 sf0611004858 6 11005857 1.40E-08 2.21E-07
vg0513935185 sf0513877729 5 13935185 2.11E-08 2.10E-06
vg0505850932 sf0505850870 5 5850932 3.09E-08 2.42E-07
vg0621437023 sf0621436026 6 21437023 3.56E-08 1.24E-07
vg0513460624 sf0513403171 5 13460624 1.20E-07 2.72E-06
vg0611018738 sf0611017739 6 11018738 3.82E-07 4.64E-07
vg0919669819 sf0919669409 9 19669819 8.39E-07 NA
vg0505645439 sf0505645377 5 5645439 5.37E-06 6.23E-08
vg1124506486 sf1124040326 11 24506486 NA 1.00E-06
vg0625104002 sf0625103005 6 25104002 NA 2.34E-06
vg0505539259 sf0505539197 5 5539259 NA 4.19E-06
vg0505673310 sf0505673248 5 5673310 NA 4.74E-06
vg0625174840 sf0625173843 6 25174840 NA 7.42E-06