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 mr1632 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
vg0506871793 sf0506871735 5 6871793 6.60E-31 5.91E-23
vg1009362967 sf1009291788 10 9362967 1.97E-16 8.16E-11
vg0506999903 sf0506999845 5 6999903 7.07E-16 3.27E-10
vg0506847027 sf0506846969 5 6847027 8.20E-16 3.12E-10
vg1213203956 sf1213201294 12 13203956 2.02E-14 7.25E-11
vg1001247140 sf1001246117 10 1247140 1.56E-13 5.11E-08
vg0514650559 sf0514593102 5 14650559 7.10E-13 2.33E-09
vg0511003990 sf0511003919 5 11003990 1.73E-12 5.75E-11
vg1002265707 sf1002264684 10 2265707 1.89E-11 6.98E-07
vg0506577678 sf0506577619 5 6577678 2.11E-10 1.84E-06
vg0507866014 sf0507865955 5 7866014 4.85E-10 2.59E-07
vg0410263984 sf0410254681 4 10263984 9.49E-10 2.45E-07
vg0517733343 sf0517672984 5 17733343 1.75E-08 2.97E-06
vg0117058038 sf0117056992 1 17058038 8.09E-08 1.24E-07
vg0506904965 sf0506904907 5 6904965 1.63E-07 3.53E-06
vg0506633865 sf0506633806 5 6633865 2.22E-07 2.79E-06
vg0327296764 sf0327289817 3 27296764 1.42E-06 1.45E-06
vg1003777399 sf1003776375 10 3777399 2.05E-06 9.02E-07
vg1223453821 sf1223420281 12 23453821 2.42E-06 3.49E-06
vg0514066405 sf0514008949 5 14066405 9.11E-06 3.03E-06
vg0714405943 sf0714404950 7 14405943 NA 3.85E-06