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 mr1331 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
vg0315356877 sf0315355524 3 15356877 3.94E-09 NA
vg0122786978 sf0122785934 1 22786978 8.23E-09 NA
vg0107188503 sf0107187503 1 7188503 1.74E-08 NA
vg1013282481 sf1013211250 10 13282481 2.47E-08 NA
vg0702073123 sf0702072124 7 2073123 3.47E-08 NA
vg1117514629 sf1117048484 11 17514629 7.32E-08 3.81E-06
vg1107376701 sf1107372446 11 7376701 9.83E-08 4.34E-06
vg0107340125 sf0107339125 1 7340125 5.95E-07 3.44E-06
vg1216729892 sf1216723846 12 16729892 3.07E-06 8.33E-07
vg0406786851 sf0406782296 4 6786851 3.59E-06 1.90E-06
vg0520272415 sf0520209888 5 20272415 5.76E-06 1.99E-06
vg1002941120 sf1002940097 10 2941120 NA 8.67E-07
vg0131964524 sf0131963480 1 31964524 NA 2.18E-06