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 mr1056 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
vg0130113615 sf0130112570 1 30113615 3.06E-10 NA
vg1218287578 sf1218259014 12 18287578 4.23E-09 NA
vg1216893818 sf1216887772 12 16893818 5.14E-09 NA
vg1222577692 sf1222544131 12 22577692 1.80E-08 NA
vg0138103681 sf0138102638 1 38103681 2.60E-08 NA
vg1222561211 sf1222527650 12 22561211 1.20E-07 6.34E-06
vg0810915114 sf0810914119 8 10915114 1.45E-07 3.29E-06
vg0138169058 sf0138168015 1 38169058 2.59E-06 NA
vg0712843936 sf0712842943 7 12843936 8.34E-06 6.88E-06
vg0610862201 sf0610861202 6 10862201 NA 2.83E-06