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 mr1191 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
vg1125519768 sf1125053607 11 25519768 1.27E-51 1.29E-33
vg1125545839 sf1125079678 11 25545839 1.15E-47 1.81E-37
vg1125509248 sf1125043087 11 25509248 2.06E-31 3.84E-21
vg1125615644 sf1125149483 11 25615644 1.49E-29 9.57E-19
vg1125609610 sf1125143449 11 25609610 7.06E-27 1.82E-22
vg1125581255 sf1125115094 11 25581255 2.97E-26 8.02E-23
vg1125596619 sf1125130458 11 25596619 5.50E-24 9.82E-19
vg1125230830 sf1124764670 11 25230830 7.76E-22 1.27E-13
vg0507714473 sf0507714414 5 7714473 1.37E-19 4.25E-10
vg1125901132 sf1125435051 11 25901132 1.03E-18 1.14E-10
vg0224605253 sf0224599384 2 24605253 4.20E-16 5.85E-13
vg1125838014 sf1125371933 11 25838014 5.36E-16 4.54E-13
vg1126331556 sf1125859969 11 26331556 7.94E-15 7.89E-09
vg1125550856 sf1125084695 11 25550856 1.17E-13 5.16E-10
vg1125547775 sf1125081614 11 25547775 1.28E-12 5.90E-16
vg1125566004 sf1125099843 11 25566004 2.70E-12 4.56E-09
vg0204430393 sf0204430390 2 4430393 5.66E-12 8.43E-09
vg1125243870 sf1124777710 11 25243870 6.06E-12 4.04E-09
vg1125148139 sf1124681979 11 25148139 1.22E-10 3.83E-19
vg1126030887 sf1125559301 11 26030887 4.75E-10 2.36E-09
vg1125791323 sf1125325244 11 25791323 7.74E-10 4.69E-11
vg0800721786 sf0800720786 8 721786 9.95E-10 NA
vg1125232324 sf1124766164 11 25232324 NA 2.35E-14
vg1125606054 sf1125139893 11 25606054 NA 2.11E-10
vg1125418435 sf1124952274 11 25418435 NA 8.90E-10
vg0113805974 sf0113804948 1 13805974 NA 2.41E-06