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 mr1142 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 2.84E-43 5.03E-21
vg1211776048 sf1211773384 12 11776048 2.18E-16 NA
vg0218132013 sf0218126144 2 18132013 2.27E-16 2.37E-07
vg0724571945 sf0724570951 7 24571945 9.23E-16 NA
vg0102127805 sf0102126805 1 2127805 1.02E-15 NA
vg1215851516 sf1215848812 12 15851516 NA 3.26E-08
vg0901048761 sf0901047761 9 1048761 NA 2.06E-07
vg0317414701 sf0317413511 3 17414701 NA 4.17E-07
vg0433192266 sf0433007154 4 33192266 NA 9.63E-07
vg1022588644 sf1022517118 10 22588644 NA 1.07E-06
vg0102116003 sf0102115003 1 2116003 NA 2.02E-06
vg1216176025 sf1216173321 12 16176025 NA 2.35E-06