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 mr1944 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
vg1219662811 sf1219634281 12 19662811 1.99E-47 2.58E-06
vg0220866078 sf0220860210 2 20866078 4.08E-46 NA
vg0726253897 sf0726252903 7 26253897 5.74E-46 NA
vg0719727916 sf0719726923 7 19727916 1.46E-45 NA
vg0232168585 sf0232162716 2 32168585 1.65E-45 NA
vg0526279747 sf0526217110 5 26279747 3.24E-41 8.22E-06
vg0518984986 sf0518922470 5 18984986 NA 7.00E-07
vg0225191431 sf0225185562 2 25191431 NA 1.26E-06
vg0223147995 sf0223142126 2 23147995 NA 2.00E-06
vg0502657346 sf0502657322 5 2657346 NA 3.11E-06
vg0502669493 sf0502669469 5 2669493 NA 4.42E-06
vg1120087774 sf1119621697 11 20087774 NA 4.84E-06
vg1102446506 sf1102442410 11 2446506 NA 5.38E-06