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 mr1811 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
vg0819603039 sf0819600326 8 19603039 4.09E-09 1.11E-07
vg0122971925 sf0122970881 1 22971925 3.02E-08 1.99E-06
vg0527928662 sf0527866019 5 27928662 6.51E-08 NA
vg0122971893 sf0122970849 1 22971893 1.10E-07 5.58E-06
vg0819356506 sf0819353793 8 19356506 1.73E-07 4.65E-07
vg1215307750 sf1215305048 12 15307750 2.13E-07 4.57E-07
vg0113652030 sf0113651004 1 13652030 9.33E-07 4.50E-07
vg0127428591 sf0127427547 1 27428591 4.63E-06 3.20E-06
vg0702696812 sf0702695813 7 2696812 9.34E-06 NA
vg0717352217 sf0717351224 7 17352217 NA 4.72E-06