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 mr1519 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
vg0115499545 sf0115498519 1 15499545 6.51E-13 2.22E-10
vg0334627622 sf0334620492 3 34627622 1.11E-09 6.00E-07
vg0116261925 sf0116260899 1 16261925 1.24E-09 9.95E-09
vg0715489455 sf0715488462 7 15489455 4.81E-09 2.99E-07
vg0814797975 sf0814795261 8 14797975 7.85E-09 1.10E-07
vg1009846344 sf1009775165 10 9846344 8.03E-09 1.02E-06
vg0334626484 sf0334619354 3 34626484 1.86E-08 NA
vg0120039531 sf0120038486 1 20039531 4.56E-08 2.77E-07
vg1119866382 sf1119400305 11 19866382 7.83E-08 1.25E-06
vg0219732180 sf0219726312 2 19732180 9.59E-08 1.14E-06
vg0615112980 sf0615111981 6 15112980 1.08E-06 4.03E-06
vg0812788939 sf0812786764 8 12788939 1.92E-06 4.45E-07
vg0601078672 sf0601077673 6 1078672 2.35E-06 6.18E-07
vg1218168761 sf1218140197 12 18168761 NA 6.11E-07
vg1010744278 sf1010673099 10 10744278 NA 3.00E-06
vg0312774141 sf0312772859 3 12774141 NA 4.71E-06
vg1218060310 sf1218031746 12 18060310 NA 4.73E-06
vg0330337817 sf0330330856 3 30337817 NA 4.74E-06