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 mr1550 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
vg0705505874 sf0705504875 7 5505874 2.42E-80 5.54E-22
vg0529267531 sf0529204886 5 29267531 8.02E-67 1.24E-12
vg0701229450 sf0701228450 7 1229450 2.79E-66 3.78E-09
vg0333028473 sf0333021343 3 33028473 2.97E-66 2.63E-09
vg0108113890 sf0108112890 1 8113890 2.67E-62 9.00E-10
vg0702584931 sf0702583932 7 2584931 1.53E-59 1.87E-09
vg0529170841 sf0529108196 5 29170841 1.81E-59 1.23E-12
vg0717004102 sf0717003109 7 17004102 8.60E-58 4.22E-09
vg0137014902 sf0137013859 1 37014902 9.19E-57 7.71E-10
vg0622627045 sf0622626048 6 22627045 4.09E-56 6.28E-09
vg0130020215 sf0130019170 1 30020215 4.68E-55 1.19E-08
vg1224163018 sf1224129472 12 24163018 9.32E-55 3.51E-08
vg1119960918 sf1119494841 11 19960918 3.17E-54 8.89E-12
vg0724353613 sf0724352619 7 24353613 1.08E-53 1.29E-08
vg0215987623 sf0215981753 2 15987623 1.02E-52 1.26E-10
vg0305879043 sf0305878043 3 5879043 1.40E-51 5.82E-09
vg0827402797 sf0827400083 8 27402797 1.73E-50 4.04E-09
vg0141182631 sf0141181588 1 41182631 2.34E-46 2.06E-08
vg1110664454 sf1110658999 11 10664454 2.21E-45 1.30E-11
vg0705321696 sf0705320697 7 5321696 NA 9.15E-09
vg0825883654 sf0825880940 8 25883654 NA 1.58E-08
vg0405251679 sf0434620208 4 5251679 NA 2.38E-08
vg0432167290 sf0431982183 4 32167290 NA 2.91E-08
vg0400004808 sf0400003808 4 4808 NA 3.90E-08
vg0116560231 sf0116559205 1 16560231 NA 2.27E-07
vg0113820611 sf0113819585 1 13820611 NA 1.06E-06
vg0409436808 sf0409427507 4 9436808 NA 8.86E-06