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 mr1750 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
vg0321242105 sf0321240615 3 21242105 3.76E-35 5.95E-18
vg0321437947 sf0321436457 3 21437947 2.17E-33 5.20E-20
vg0317793674 sf0317792456 3 17793674 7.26E-29 3.32E-15
vg0317654172 sf0317652954 3 17654172 1.31E-27 1.10E-15
vg0318193307 sf0318192089 3 18193307 1.23E-23 9.83E-10
vg0318763839 sf0318762599 3 18763839 2.48E-21 3.43E-11
vg0320905869 sf0320904379 3 20905869 7.78E-21 6.43E-09
vg0320619051 sf0320617561 3 20619051 4.91E-20 3.15E-10
vg0319509282 sf0319507793 3 19509282 2.92E-19 2.04E-08
vg0320944374 sf0320942884 3 20944374 3.91E-19 4.60E-11
vg0317655045 sf0317653827 3 17655045 5.36E-18 2.13E-08
vg0319080319 sf0319079079 3 19080319 1.23E-17 6.37E-10
vg0318765858 sf0318764618 3 18765858 4.65E-17 1.25E-07
vg0319674500 sf0319673011 3 19674500 5.91E-17 1.15E-07
vg0320827730 sf0320826240 3 20827730 2.65E-15 6.28E-08
vg0320046683 sf0320045194 3 20046683 5.55E-15 2.30E-09
vg0321132765 sf0321131275 3 21132765 2.78E-14 7.80E-08
vg0318955179 sf0318953939 3 18955179 4.56E-14 7.93E-08
vg0318419210 sf0318417992 3 18419210 1.29E-13 6.85E-08
vg0318061429 sf0318060211 3 18061429 2.52E-12 1.22E-07
vg0324100933 sf0324099012 3 24100933 3.92E-12 2.78E-10
vg0327963836 sf0327956890 3 27963836 6.19E-11 1.67E-07
vg0806150747 sf0806149752 8 6150747 3.68E-09 4.61E-09
vg0321533612 sf0321532122 3 21533612 NA 1.86E-09
vg0802219948 sf0802218951 8 2219948 NA 6.39E-08