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 mr1369 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
vg0919141927 sf0919141516 9 19141927 1.22E-07 1.22E-07
vg0709448532 sf0709447538 7 9448532 1.35E-07 1.35E-07
vg1114618741 sf1114155059 11 14618741 1.02E-06 1.02E-06
vg0716279747 sf0716278754 7 16279747 1.28E-06 1.28E-06
vg0202968896 sf0202968894 2 2968896 1.52E-06 1.52E-06
vg0603303648 sf0603302649 6 3303648 1.62E-06 1.62E-06
vg0716252058 sf0716251065 7 16252058 1.74E-06 1.74E-06
vg0727589348 sf0727588354 7 27589348 1.93E-06 1.93E-06
vg0516508609 sf0516451091 5 16508609 2.07E-06 2.07E-06
vg0715026108 sf0715025115 7 15026108 3.11E-06 3.11E-06
vg0312184618 sf0312183336 3 12184618 3.12E-06 3.12E-06
vg1023172834 sf1023101306 10 23172834 3.16E-06 3.16E-06
vg0420718113 sf0420546156 4 20718113 3.82E-06 3.82E-06
vg0717084739 sf0717083746 7 17084739 4.86E-06 4.86E-06
vg0316786845 sf0316785719 3 16786845 6.29E-06 6.29E-06