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 mr1984 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
vg0326027307 sf0326025326 3 26027307 3.46E-08 1.85E-07
vg0908281367 sf0908280367 9 8281367 4.77E-08 NA
vg0142744953 sf0142743909 1 42744953 7.87E-08 1.49E-07
vg0142709816 sf0142708772 1 42709816 8.22E-08 1.14E-07
vg0317919384 sf0317918166 3 17919384 9.18E-08 NA
vg1119521777 sf1119055465 11 19521777 3.10E-07 6.23E-06
vg0315356877 sf0315355524 3 15356877 3.73E-07 2.08E-06
vg1227059828 sf1227026227 12 27059828 1.79E-06 3.21E-06
vg1014597243 sf1014526009 10 14597243 1.97E-06 2.07E-06
vg1222329942 sf1222296381 12 22329942 NA 2.30E-06
vg0727511786 sf0727510792 7 27511786 NA 3.55E-06