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 mr1768 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
vg0910147323 sf0910146322 9 10147323 1.42E-09 NA
vg1010548109 sf1010476930 10 10548109 2.12E-09 1.59E-06
vg1217854401 sf1217825835 12 17854401 2.45E-09 2.46E-07
vg1005035532 sf1005052069 10 5035532 1.60E-08 NA
vg1217691881 sf1217685836 12 17691881 1.67E-08 NA
vg1214362394 sf1214359734 12 14362394 2.15E-08 2.46E-06
vg1005063902 sf1005080439 10 5063902 2.73E-08 6.82E-07
vg0903361943 sf0903360943 9 3361943 2.02E-07 2.78E-06
vg1022582083 sf1022510557 10 22582083 2.08E-07 4.82E-06
vg1002271984 sf1002270961 10 2271984 3.76E-07 5.73E-06
vg0906274104 sf0906273104 9 6274104 4.15E-07 8.22E-07
vg0719200609 sf0719199616 7 19200609 6.74E-07 4.42E-06
vg0620733763 sf0620732766 6 20733763 6.91E-07 2.44E-06
vg0141973334 sf0141972291 1 41973334 1.75E-06 2.61E-06
vg0622937793 sf0622936796 6 22937793 2.20E-06 4.99E-06
vg0206099857 sf0206099857 2 6099857 2.52E-06 1.21E-06
vg0719492480 sf0719491487 7 19492480 5.89E-06 1.16E-06
vg0911047829 sf0911046828 9 11047829 6.94E-06 1.22E-06
vg1117431160 sf1116965015 11 17431160 9.09E-06 NA
vg1128136971 sf1127613750 11 28136971 NA 1.48E-06