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 mr1900 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
vg1125118463 sf1124652303 11 25118463 4.21E-40 1.82E-31
vg1124618323 sf1124152163 11 24618323 1.08E-19 7.62E-08
vg0105132129 sf0105131129 1 5132129 8.09E-19 1.47E-08
vg0619629228 sf0619628231 6 19629228 1.56E-18 7.29E-07
vg1013067084 sf1012995899 10 13067084 7.95E-18 NA
vg1125432386 sf1124966225 11 25432386 1.06E-17 1.77E-08
vg1124875808 sf1124409648 11 24875808 1.32E-17 5.16E-13
vg1124935001 sf1124468841 11 24935001 1.98E-17 1.86E-13
vg1124989458 sf1124523298 11 24989458 4.15E-17 1.63E-18
vg1125085953 sf1124619793 11 25085953 5.89E-17 1.12E-10
vg0716934852 sf0716933859 7 16934852 4.55E-15 8.59E-08
vg1125602304 sf1125136143 11 25602304 9.61E-15 9.71E-08
vg1125113953 sf1124647793 11 25113953 NA 3.17E-15
vg1125131895 sf1124665735 11 25131895 NA 3.61E-14
vg1125080303 sf1124614143 11 25080303 NA 1.40E-12
vg1125113390 sf1124647230 11 25113390 NA 4.98E-11
vg1125089512 sf1124623352 11 25089512 NA 1.27E-10
vg1125084128 sf1124617968 11 25084128 NA 6.70E-09
vg1125004703 sf1124538543 11 25004703 NA 8.41E-09
vg1125389716 sf1124923555 11 25389716 NA 3.15E-08
vg1127384160 sf1126912547 11 27384160 NA 1.36E-07
vg0327532510 sf0327525563 3 27532510 NA 1.47E-07
vg1124874824 sf1124408664 11 24874824 NA 1.89E-07
vg0910580422 sf0910579421 9 10580422 NA 2.30E-07
vg0712821619 sf0712820626 7 12821619 NA 4.09E-07
vg0813435160 sf0813432713 8 13435160 NA 9.74E-07
vg1125038758 sf1124572598 11 25038758 NA 1.50E-06