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 mr1594 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
vg1014788162 sf1014716928 10 14788162 1.17E-78 2.35E-09
vg0332485398 sf0332478271 3 32485398 1.64E-75 NA
vg0104705923 sf0104704923 1 4705923 1.66E-74 NA
vg0827202544 sf0827199830 8 27202544 1.10E-73 NA
vg0917434356 sf0917433355 9 17434356 5.22E-73 NA
vg0528836237 sf0528773592 5 28836237 NA 1.36E-06
vg1017093627 sf1017022399 10 17093627 NA 1.98E-06
vg0106205427 sf0106204427 1 6205427 NA 2.08E-06
vg0918876795 sf0918875795 9 18876795 NA 2.46E-06
vg0224488705 sf0224482836 2 24488705 NA 2.50E-06
vg0805970880 sf0805969883 8 5970880 NA 3.29E-06
vg0717192832 sf0717191839 7 17192832 NA 3.60E-06
vg0806013173 sf0806012176 8 6013173 NA 3.81E-06
vg0918880163 sf0918879163 9 18880163 NA 3.89E-06