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 mr1039 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
vg0506847525 sf0506847467 5 6847525 4.24E-93 1.96E-56
vg0506871793 sf0506871735 5 6871793 3.55E-87 1.38E-54
vg1001247140 sf1001246117 10 1247140 1.90E-34 2.66E-08
vg1009362967 sf1009291788 10 9362967 1.10E-30 8.72E-09
vg0513833782 sf0513776326 5 13833782 1.78E-24 1.01E-10
vg0512332611 sf0512332541 5 12332611 1.21E-23 3.18E-11
vg0509887388 sf0509887317 5 9887388 6.05E-23 1.49E-10
vg0509650627 sf0509650556 5 9650627 1.80E-22 3.57E-10
vg0412231824 sf0412222535 4 12231824 1.04E-21 3.15E-06
vg1213203956 sf1213201294 12 13203956 2.49E-20 2.72E-06
vg0320268646 sf0320267157 3 20268646 2.00E-18 6.58E-07
vg0506577678 sf0506577619 5 6577678 3.59E-16 3.38E-07
vg0506060649 sf0506060588 5 6060649 1.22E-15 8.69E-07
vg0517733343 sf0517672984 5 17733343 2.02E-12 4.36E-06
vg0506623100 sf0506623041 5 6623100 3.63E-12 9.72E-07
vg0505429323 sf0505429301 5 5429323 1.55E-11 2.83E-06
vg0506866456 sf0506866398 5 6866456 1.15E-10 4.73E-11
vg0506944661 sf0506944603 5 6944661 4.34E-10 9.80E-09
vg0507887823 sf0507887764 5 7887823 5.06E-10 5.86E-09
vg0514649039 sf0514591582 5 14649039 1.31E-09 1.05E-06
vg0804370126 sf0804369129 8 4370126 1.49E-07 4.24E-06
vg0407766376 sf0407761644 4 7766376 NA 1.06E-08
vg1010999655 sf1010928475 10 10999655 NA 2.44E-06
vg0523542913 sf0523480334 5 23542913 NA 3.17E-06