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 mr1050 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
vg0330926836 sf0330919723 3 30926836 4.40E-14 1.54E-08
vg0330744944 sf0330737831 3 30744944 3.21E-13 9.92E-09
vg1105377516 sf1105373267 11 5377516 4.07E-09 NA
vg0214942349 sf0214936479 2 14942349 1.98E-08 3.99E-06
vg1213154999 sf1213152337 12 13154999 2.37E-08 NA
vg0427970215 sf0427785079 4 27970215 3.85E-08 NA
vg1124076491 sf1123610361 11 24076491 2.16E-07 1.25E-06
vg1022145421 sf1022073895 10 22145421 3.62E-07 3.12E-06
vg1124078519 sf1123612389 11 24078519 2.03E-06 3.55E-06
vg1120315862 sf1119849786 11 20315862 2.47E-06 5.42E-07
vg1212736885 sf1212734224 12 12736885 4.42E-06 4.57E-06
vg0608906632 sf0608905633 6 8906632 6.70E-06 3.92E-06
vg1015204035 sf1015132803 10 15204035 NA 4.26E-06
vg0613848822 sf0613847823 6 13848822 NA 4.48E-06
vg0120215560 sf0120214515 1 20215560 NA 5.84E-06