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 mr1211 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
vg0610539571 sf0610538572 6 10539571 7.63E-34 6.38E-25
vg0610585326 sf0610584327 6 10585326 3.42E-32 2.34E-25
vg0610608095 sf0610607096 6 10608095 9.89E-31 1.96E-23
vg0610567030 sf0610566031 6 10567030 3.44E-28 2.99E-22
vg0610645257 sf0610644258 6 10645257 1.58E-19 3.85E-16
vg0610684751 sf0610683752 6 10684751 1.88E-14 1.78E-09
vg0610119624 sf0610118625 6 10119624 2.92E-14 3.21E-09
vg0610553290 sf0610552291 6 10553290 3.22E-14 5.17E-11
vg0617611502 sf0617610505 6 17611502 1.58E-13 5.36E-09
vg0610685381 sf0610684382 6 10685381 1.59E-13 2.61E-12
vg0610278152 sf0610277153 6 10278152 2.48E-13 2.00E-13
vg0610687475 sf0610686476 6 10687475 5.29E-13 1.16E-09
vg0610676252 sf0610675253 6 10676252 5.75E-12 9.25E-09
vg0610740899 sf0610739900 6 10740899 7.43E-12 2.68E-09
vg0614798821 sf0614797822 6 14798821 2.69E-10 1.76E-07
vg0611098102 sf0611097103 6 11098102 3.16E-09 9.99E-09
vg0611645542 sf0611644543 6 11645542 3.24E-09 2.22E-08
vg0610613420 sf0610612421 6 10613420 1.98E-08 1.61E-07
vg0629086139 sf0629085141 6 29086139 2.32E-08 7.69E-07
vg0610318906 sf0610317907 6 10318906 3.44E-08 1.93E-07
vg0617815461 sf0617814464 6 17815461 6.96E-08 3.44E-08
vg0610642043 sf0610641044 6 10642043 2.38E-07 1.14E-07
vg0114075940 sf0114074914 1 14075940 7.26E-07 NA
vg1213254610 sf1213251948 12 13254610 1.70E-06 9.69E-07
vg0613121363 sf0613120364 6 13121363 NA 3.02E-07
vg0421455343 sf0421283394 4 21455343 NA 8.58E-07
vg0117018913 sf0117017867 1 17018913 NA 8.32E-06