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 mr1203 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
vg0406995300 sf0406990571 4 6995300 8.70E-13 3.36E-09
vg0406944785 sf0406940053 4 6944785 1.80E-12 9.31E-10
vg0616169045 sf0616168047 6 16169045 1.89E-11 6.41E-07
vg0412100387 sf0412091098 4 12100387 2.42E-11 3.78E-08
vg0406620026 sf0406615470 4 6620026 9.77E-11 1.18E-06
vg0406592386 sf0406587830 4 6592386 2.95E-10 4.06E-08
vg0618618072 sf0618617075 6 18618072 8.68E-10 1.75E-08
vg0406592431 sf0406587875 4 6592431 9.75E-10 1.97E-07
vg1218763524 sf1218734959 12 18763524 2.07E-09 1.20E-09
vg1205463941 sf1205462927 12 5463941 3.65E-09 5.84E-07
vg0402523133 sf0402518738 4 2523133 4.89E-09 1.82E-06
vg0706671410 sf0706670415 7 6671410 8.26E-09 1.10E-09
vg0616244147 sf0616243149 6 16244147 3.10E-08 1.23E-06
vg0223166690 sf0223160821 2 23166690 5.08E-08 NA
vg0407665649 sf0407660916 4 7665649 5.25E-08 1.51E-10
vg1000993495 sf1000992471 10 993495 7.53E-07 5.14E-07
vg0614933791 sf0614932792 6 14933791 1.04E-06 6.55E-07
vg1226826332 sf1226792731 12 26826332 1.19E-06 2.38E-08
vg1208693304 sf1208690711 12 8693304 3.84E-06 3.41E-07
vg1210467503 sf1210464916 12 10467503 6.96E-06 4.63E-08
vg0715307926 sf0715306933 7 15307926 7.45E-06 4.61E-07
vg0709331066 sf0709330072 7 9331066 NA 9.54E-07
vg0526374490 sf0526311853 5 26374490 NA 1.36E-06
vg0813085446 sf0813083076 8 13085446 NA 8.22E-06