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 mr1423 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
vg0217095828 sf0217089958 2 17095828 2.87E-53 1.59E-24
vg0216732442 sf0216726572 2 16732442 2.38E-45 4.19E-13
vg0216623044 sf0216617174 2 16623044 3.89E-43 2.16E-13
vg1210765292 sf1210762658 12 10765292 1.02E-32 NA
vg0310111382 sf0310110318 3 10111382 8.66E-32 NA
vg0310101976 sf0310100912 3 10101976 8.71E-32 2.82E-06
vg0804494511 sf0804493514 8 4494511 3.26E-31 NA
vg0714328687 sf0714327694 7 14328687 1.74E-26 1.41E-06
vg0217233417 sf0217227547 2 17233417 NA 1.05E-13
vg0217327456 sf0217321586 2 17327456 NA 1.02E-08
vg1114473442 sf1114009759 11 14473442 NA 1.23E-08
vg0812023942 sf0812022947 8 12023942 NA 1.45E-08
vg0216761078 sf0216755208 2 16761078 NA 4.72E-08
vg1005364262 sf1005380799 10 5364262 NA 7.21E-08
vg1105770829 sf1105766581 11 5770829 NA 1.87E-07
vg0214316674 sf0214310804 2 14316674 NA 2.75E-07
vg0217520029 sf0217514159 2 17520029 NA 9.40E-07
vg0216773376 sf0216767506 2 16773376 NA 1.38E-06
vg0217316653 sf0217310783 2 17316653 NA 2.87E-06
vg0719105731 sf0719104738 7 19105731 NA 4.37E-06
vg0900337327 sf0900336327 9 337327 NA 4.78E-06