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 mr1951 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
vg0106677498 sf0106676498 1 6677498 7.26E-60 8.80E-37
vg0106688727 sf0106687727 1 6688727 2.38E-59 1.44E-36
vg0106691928 sf0106690928 1 6691928 3.13E-59 5.05E-37
vg0106607583 sf0106606583 1 6607583 8.20E-21 2.62E-10
vg0106684462 sf0106683462 1 6684462 1.50E-17 4.16E-15
vg0106689232 sf0106688232 1 6689232 3.41E-17 3.67E-15
vg0107100004 sf0107099004 1 7100004 6.34E-17 2.72E-10
vg0108087881 sf0108086881 1 8087881 2.37E-16 1.93E-07
vg0105363790 sf0105362790 1 5363790 2.99E-16 1.35E-07
vg0107074175 sf0107073175 1 7074175 4.49E-16 7.15E-08
vg0105276912 sf0105275912 1 5276912 8.81E-16 1.09E-09
vg0107076196 sf0107075196 1 7076196 1.56E-15 2.06E-07
vg0402919496 sf0402915102 4 2919496 3.16E-13 2.69E-08
vg0105626001 sf0105625001 1 5626001 4.48E-13 6.78E-09
vg0106826782 sf0106825782 1 6826782 1.56E-12 7.10E-08
vg0103935216 sf0103934216 1 3935216 3.06E-12 5.77E-07
vg0105622335 sf0105621335 1 5622335 1.22E-11 1.24E-08
vg0421520546 sf0421348597 4 21520546 1.77E-08 1.21E-06
vg0424217937 sf0424032798 4 24217937 1.89E-08 1.07E-06
vg0106184160 sf0106183160 1 6184160 2.09E-07 7.85E-08
vg0106669651 sf0106668651 1 6669651 NA 1.61E-14
vg0106873407 sf0106872407 1 6873407 NA 3.66E-13
vg1215867954 sf1215865250 12 15867954 NA 1.84E-06
vg0106679567 sf0106678567 1 6679567 NA 1.92E-06
vg1015148329 sf1015077097 10 15148329 NA 4.94E-06