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 mr1124 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
vg0222719586 sf0222713717 2 22719586 5.03E-42 9.67E-26
vg0222727819 sf0222721950 2 22727819 9.05E-42 2.62E-26
vg0223736656 sf0223730787 2 23736656 2.03E-12 9.73E-10
vg0222849899 sf0222844030 2 22849899 4.07E-12 7.25E-09
vg0223683609 sf0223677740 2 23683609 7.50E-12 1.03E-08
vg0610884350 sf0610883351 6 10884350 1.08E-11 7.61E-06
vg0223453927 sf0223448058 2 23453927 3.80E-11 NA
vg0222671915 sf0222666046 2 22671915 4.78E-11 5.15E-11
vg0224274079 sf0224268210 2 24274079 2.37E-10 4.45E-06
vg0223166690 sf0223160821 2 23166690 3.91E-10 4.51E-06
vg0610566738 sf0610565739 6 10566738 9.29E-09 2.64E-06
vg0222802022 sf0222796153 2 22802022 2.43E-08 5.00E-06
vg0222857256 sf0222851387 2 22857256 7.29E-08 9.39E-07
vg0218598781 sf0218592912 2 18598781 1.81E-07 4.41E-06
vg0222620162 sf0222614293 2 22620162 2.20E-07 2.86E-06
vg0223720133 sf0223714264 2 23720133 NA 2.64E-06