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 mr1138 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
vg0916974525 sf0916973524 9 16974525 3.97E-19 3.01E-06
vg0218063030 sf0218057161 2 18063030 5.28E-18 1.20E-07
vg0430060754 sf0429875625 4 30060754 5.90E-18 NA
vg0724527960 sf0724526966 7 24527960 1.11E-16 5.10E-10
vg0607159174 sf0607158175 6 7159174 1.34E-16 NA
vg0429937896 sf0429752763 4 29937896 1.43E-16 NA
vg0724560524 sf0724559530 7 24560524 1.48E-16 5.03E-10
vg0429945960 sf0429760827 4 29945960 1.12E-15 1.80E-06
vg0217541786 sf0217535916 2 17541786 3.36E-15 4.55E-08
vg0916858916 sf0916857915 9 16858916 7.57E-15 8.45E-08
vg0332114927 sf0332107804 3 32114927 3.61E-14 3.61E-06
vg0332173744 sf0332166621 3 32173744 1.15E-13 1.77E-06
vg0218033645 sf0218027776 2 18033645 1.85E-13 2.06E-08
vg0628726342 sf0628725344 6 28726342 1.59E-11 NA
vg0918173779 sf0918172778 9 18173779 NA 1.71E-11
vg0916234298 sf0916233297 9 16234298 NA 1.74E-11
vg0800596392 sf0800595392 8 596392 NA 2.24E-10
vg0800579516 sf0800578516 8 579516 NA 5.56E-10
vg0724482522 sf0724481528 7 24482522 NA 6.65E-09
vg0724561179 sf0724560185 7 24561179 NA 4.71E-08
vg0218055998 sf0218050129 2 18055998 NA 2.18E-07
vg0218432703 sf0218426834 2 18432703 NA 2.49E-07
vg0800648461 sf0800647461 8 648461 NA 3.78E-07
vg0800651989 sf0800650989 8 651989 NA 4.80E-07
vg0916752683 sf0916751682 9 16752683 NA 5.80E-07
vg0918969222 sf0918968222 9 18969222 NA 6.06E-07
vg1004393497 sf1004410035 10 4393497 NA 9.00E-07
vg0513325546 sf0513268468 5 13325546 NA 9.06E-07
vg0331310984 sf0331303869 3 31310984 NA 2.50E-06
vg0331267616 sf0331260501 3 31267616 NA 2.80E-06