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 mr1676 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
vg0107047780 sf0107046780 1 7047780 6.02E-15 1.05E-07
vg0107057474 sf0107056474 1 7057474 2.23E-14 4.17E-08
vg0606395061 sf0606394062 6 6395061 1.44E-12 9.66E-07
vg0301180037 sf0301179035 3 1180037 1.97E-12 NA
vg1223208705 sf1223175165 12 23208705 3.71E-12 3.82E-06
vg0619981830 sf0619980833 6 19981830 5.76E-12 NA
vg0611847509 sf0611846510 6 11847509 1.23E-11 1.99E-07
vg0128723861 sf0128722816 1 28723861 4.07E-11 5.54E-07
vg0139730184 sf0139729141 1 39730184 4.32E-11 1.37E-06
vg0515429615 sf0515372156 5 15429615 5.20E-11 2.81E-06
vg0827882271 sf0827879557 8 27882271 9.40E-11 3.52E-06
vg0130377630 sf0130376586 1 30377630 1.38E-10 1.48E-06
vg1221699222 sf1221665769 12 21699222 2.31E-10 2.90E-07
vg0520296341 sf0520233814 5 20296341 2.46E-10 5.11E-09
vg1103989226 sf1103985128 11 3989226 2.94E-10 4.30E-07
vg0918918596 sf0918917596 9 18918596 5.13E-10 NA
vg0606708075 sf0606707076 6 6708075 6.62E-10 1.22E-06
vg1011513758 sf1011442577 10 11513758 7.67E-10 1.13E-06
vg0430189232 sf0430004104 4 30189232 8.00E-10 4.03E-06
vg0208396849 sf0208396848 2 8396849 5.59E-09 1.49E-06
vg0124418602 sf0124417558 1 24418602 2.01E-08 2.09E-06
vg0817805780 sf0817803067 8 17805780 1.56E-07 2.70E-06
vg0322267088 sf0322265595 3 22267088 NA 9.89E-07
vg0316348387 sf0316347034 3 16348387 NA 2.05E-06
vg0317372993 sf0317371803 3 17372993 NA 2.22E-06
vg0408196898 sf0408192172 4 8196898 NA 2.83E-06