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 mr1683 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
vg0421013424 sf0420841477 4 21013424 2.23E-09 9.19E-07
vg0421030366 sf0420858419 4 21030366 3.43E-09 3.39E-07
vg0819602446 sf0819599733 8 19602446 9.00E-09 1.62E-06
vg0122971925 sf0122970881 1 22971925 2.34E-08 7.24E-06
vg0410770678 sf0410761379 4 10770678 2.60E-08 5.98E-06
vg0407320870 sf0407316140 4 7320870 4.17E-08 NA
vg0421299708 sf0421127762 4 21299708 5.04E-08 3.54E-06
vg0709448532 sf0709447538 7 9448532 1.12E-07 3.26E-07
vg0420718113 sf0420546156 4 20718113 1.28E-07 2.72E-06
vg0704732672 sf0704731673 7 4732672 6.44E-07 4.63E-06
vg0421384856 sf0421212909 4 21384856 9.05E-07 3.56E-06
vg1104596684 sf1104592586 11 4596684 5.57E-06 3.30E-06
vg0113652030 sf0113651004 1 13652030 NA 2.96E-06