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 mr1333 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
vg1211533514 sf1211530850 12 11533514 4.95E-08 4.95E-08
vg0607216580 sf0607215581 6 7216580 6.10E-08 6.11E-08
vg1006755863 sf1006771486 10 6755863 5.95E-07 5.95E-07
vg0223262220 sf0223256351 2 23262220 8.81E-07 8.81E-07
vg1011536743 sf1011465562 10 11536743 1.08E-06 1.08E-06
vg0805790429 sf0805789432 8 5790429 1.49E-06 1.49E-06
vg1214590110 sf1214587450 12 14590110 1.56E-06 1.56E-06
vg0729239915 sf0729238923 7 29239915 1.67E-06 1.67E-06
vg0432263043 sf0432077936 4 32263043 1.84E-06 1.84E-06
vg1122663480 sf1122197351 11 22663480 2.11E-06 2.11E-06
vg0421022965 sf0420851018 4 21022965 2.25E-06 2.25E-06
vg0132410982 sf0132409938 1 32410982 2.26E-06 2.26E-06
vg0400644328 sf0400643327 4 644328 2.70E-06 2.70E-06
vg0315630241 sf0315628888 3 15630241 2.85E-06 2.85E-06
vg1220263690 sf1220235132 12 20263690 3.75E-06 3.75E-06
vg0209430779 sf0209430777 2 9430779 4.42E-06 4.42E-06
vg1216565349 sf1216562642 12 16565349 4.43E-06 4.43E-06
vg0107647091 sf0107646091 1 7647091 4.68E-06 4.68E-06
vg0312969719 sf0312968437 3 12969719 4.80E-06 4.80E-06