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 mr1410 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
vg0417244171 sf0417072212 4 17244171 5.30E-24 8.77E-11
vg0519939017 sf0519876493 5 19939017 2.88E-21 9.41E-09
vg0406753488 sf0406748934 4 6753488 2.65E-20 1.16E-07
vg0211588654 sf0211588650 2 11588654 6.27E-19 6.85E-09
vg0905616909 sf0905615909 9 5616909 2.48E-18 3.24E-06
vg0905685207 sf0905684207 9 5685207 3.48E-18 1.07E-06
vg0403055424 sf0403051028 4 3055424 9.12E-18 2.47E-06
vg0200785919 sf0200785919 2 785919 6.25E-17 1.10E-06
vg0821086229 sf0821083516 8 21086229 2.79E-16 7.29E-07
vg0614481201 sf0614480202 6 14481201 3.73E-16 2.83E-06
vg0314107109 sf0314105798 3 14107109 5.83E-16 2.60E-07
vg0516124006 sf0516066490 5 16124006 3.85E-15 1.07E-06
vg0818028929 sf0818026216 8 18028929 4.08E-14 1.95E-06
vg0509755928 sf0509755857 5 9755928 9.43E-13 1.10E-06
vg0208516943 sf0208516942 2 8516943 1.51E-12 2.15E-07
vg0109361051 sf0109360027 1 9361051 2.63E-12 NA
vg0514136632 sf0514079176 5 14136632 6.00E-12 2.20E-06
vg0407098060 sf0407093330 4 7098060 1.79E-11 1.01E-08
vg0417240491 sf0417068532 4 17240491 NA 9.45E-08
vg1217945266 sf1217916700 12 17945266 NA 1.00E-07
vg0417064731 sf0416892773 4 17064731 NA 3.08E-07
vg0403205829 sf0403201432 4 3205829 NA 4.46E-07
vg1220761649 sf1220728197 12 20761649 NA 7.14E-07
vg0412124797 sf0412115508 4 12124797 NA 7.21E-07
vg0418867182 sf0418695227 4 18867182 NA 9.28E-07
vg0818744396 sf0818741683 8 18744396 NA 1.48E-06
vg0816725186 sf0816722472 8 16725186 NA 4.02E-06