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 mr1078 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
vg0610471672 sf0610470673 6 10471672 1.46E-63 2.38E-42
vg0610566371 sf0610565372 6 10566371 1.54E-63 4.61E-44
vg0610460975 sf0610459976 6 10460975 7.33E-21 1.26E-15
vg0610435285 sf0610434286 6 10435285 2.87E-20 9.00E-19
vg0610433780 sf0610432781 6 10433780 5.25E-19 3.53E-17
vg0610685381 sf0610684382 6 10685381 1.52E-18 1.40E-12
vg0610974808 sf0610973809 6 10974808 5.37E-17 1.44E-11
vg0610679932 sf0610678933 6 10679932 1.37E-16 7.50E-17
vg0610367407 sf0610366408 6 10367407 1.98E-16 1.88E-10
vg0920308003 sf0920307522 9 20308003 5.81E-15 1.84E-07
vg0612086046 sf0612085047 6 12086046 9.21E-14 1.41E-09
vg0610609111 sf0610608112 6 10609111 9.77E-14 3.18E-10
vg0610556004 sf0610555005 6 10556004 1.29E-13 3.95E-15
vg0610429643 sf0610428644 6 10429643 1.32E-13 2.32E-09
vg0610419198 sf0610418199 6 10419198 1.90E-13 2.11E-10
vg0611098102 sf0611097103 6 11098102 4.69E-13 1.03E-09
vg0610613420 sf0610612421 6 10613420 8.78E-13 1.71E-09
vg0611561542 sf0611560543 6 11561542 1.91E-10 1.94E-09
vg0615150907 sf0615149908 6 15150907 4.11E-10 3.22E-09
vg0611510915 sf0611509916 6 11510915 1.35E-09 2.24E-07
vg0610119083 sf0610118084 6 10119083 2.88E-09 5.34E-12
vg0610205289 sf0610204290 6 10205289 1.33E-08 4.06E-08
vg0613809145 sf0613808146 6 13809145 1.82E-08 8.08E-08
vg0618988041 sf0618987044 6 18988041 NA 6.40E-09
vg0611634340 sf0611633341 6 11634340 NA 4.23E-08