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 mr1022 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
vg1215854982 sf1215852278 12 15854982 5.47E-76 1.43E-36
vg1215854444 sf1215851740 12 15854444 3.26E-74 3.33E-34
vg1209571445 sf1209568854 12 9571445 1.20E-56 2.18E-21
vg1209294462 sf1209291871 12 9294462 9.51E-55 5.24E-24
vg1223872806 sf1223839259 12 23872806 6.71E-45 2.45E-10
vg1223827289 sf1223793742 12 23827289 1.12E-41 1.19E-10
vg1212726422 sf1212723761 12 12726422 1.41E-30 1.39E-08
vg1219911712 sf1219883182 12 19911712 2.57E-25 1.42E-06
vg0410423427 sf0410414126 4 10423427 4.58E-24 1.19E-06
vg1017847198 sf1017775971 10 17847198 6.54E-22 2.49E-07
vg1216192863 sf1216190159 12 16192863 6.53E-18 2.60E-14
vg0217462843 sf0217456973 2 17462843 7.22E-18 7.05E-07
vg1216680196 sf1216674150 12 16680196 2.40E-16 2.54E-08
vg1207827697 sf1207825103 12 7827697 1.10E-15 7.62E-13
vg1216282451 sf1216279747 12 16282451 1.74E-13 4.26E-07
vg1215237966 sf1215235263 12 15237966 1.02E-12 5.85E-07
vg1215359540 sf1215356838 12 15359540 1.08E-12 2.55E-08
vg1216279538 sf1216276834 12 16279538 NA 3.16E-08
vg1205718847 sf1205716942 12 5718847 NA 7.82E-08
vg0400174925 sf0400173925 4 174925 NA 1.88E-07
vg0327914592 sf0327907646 3 27914592 NA 4.09E-07
vg1214147827 sf1214145167 12 14147827 NA 4.42E-07
vg1215520105 sf1215517402 12 15520105 NA 4.69E-07
vg1214841073 sf1214838414 12 14841073 NA 1.05E-06