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 mr1422 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
vg0506207863 sf0506207802 5 6207863 6.18E-12 1.21E-09
vg1215106857 sf1215104194 12 15106857 3.49E-11 9.88E-07
vg0205500892 sf0205500892 2 5500892 1.70E-10 NA
vg0403315819 sf0403311422 4 3315819 2.04E-10 1.54E-08
vg0223262220 sf0223256351 2 23262220 1.03E-09 8.22E-07
vg0624774901 sf0624773904 6 24774901 1.03E-09 1.52E-07
vg1122937279 sf1122471150 11 22937279 1.68E-09 2.88E-06
vg0314969789 sf0314968436 3 14969789 2.81E-09 NA
vg0502976477 sf0502976453 5 2976477 5.02E-09 2.35E-06
vg1214273942 sf1214271282 12 14273942 7.67E-09 3.48E-06
vg0312772189 sf0312770907 3 12772189 8.60E-09 1.29E-06
vg0335284080 sf0335276949 3 35284080 2.99E-08 2.32E-06
vg0315240706 sf0315239353 3 15240706 1.53E-07 4.90E-06