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 mr1778 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
vg1215869969 sf1215867265 12 15869969 1.42E-38 1.58E-19
vg1211103816 sf1211101182 12 11103816 1.75E-16 NA
vg0724570350 sf0724569356 7 24570350 2.01E-14 NA
vg0218132013 sf0218126144 2 18132013 3.38E-14 1.63E-06
vg0919147683 sf0919147272 9 19147683 1.65E-13 NA
vg1216138955 sf1216136251 12 16138955 NA 2.90E-09
vg0901048761 sf0901047761 9 1048761 NA 1.14E-07
vg1216127459 sf1216124755 12 16127459 NA 3.36E-06
vg1022588644 sf1022517118 10 22588644 NA 3.38E-06
vg1218663003 sf1218634438 12 18663003 NA 4.74E-06