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 mr1815 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
vg0434239826 sf0434054722 4 34239826 1.37E-12 2.14E-06
vg0129472791 sf0129471746 1 29472791 5.87E-12 NA
vg1213171598 sf1213168936 12 13171598 1.27E-10 NA
vg0421939437 sf0421767488 4 21939437 3.67E-10 NA
vg0113567574 sf0113566548 1 13567574 4.28E-10 NA
vg1118128662 sf1117662520 11 18128662 1.95E-07 1.13E-06
vg1215354440 sf1215351738 12 15354440 2.27E-06 3.53E-06
vg0416201160 sf0416029193 4 16201160 2.67E-06 NA
vg1215582061 sf1215579358 12 15582061 4.06E-06 5.65E-06
vg0107647091 sf0107646091 1 7647091 NA 1.58E-06
vg0113458723 sf0113457697 1 13458723 NA 1.58E-06
vg0316819218 sf0316818092 3 16819218 NA 3.99E-06