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 mr1881 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
vg1217551907 sf1217545862 12 17551907 5.40E-11 5.40E-11
vg1203150141 sf1203149144 12 3150141 4.36E-09 4.36E-09
vg0818421321 sf0818418608 8 18421321 1.64E-08 1.64E-08
vg1211121901 sf1211119265 12 11121901 2.07E-08 2.07E-08
vg0108533994 sf0108532994 1 8533994 1.11E-07 1.11E-07
vg1128496224 sf1127973003 11 28496224 1.46E-07 1.46E-07
vg0318761133 sf0318759893 3 18761133 7.90E-07 7.90E-07
vg0817796299 sf0817793586 8 17796299 8.87E-07 8.87E-07
vg0209846808 sf0209846806 2 9846808 9.30E-07 9.30E-07
vg0322388599 sf0322387088 3 22388599 1.00E-06 1.00E-06
vg0124471054 sf0124470010 1 24471054 1.05E-06 1.05E-06
vg0921518391 sf0921517910 9 21518391 1.24E-06 1.24E-06
vg1223881012 sf1223847465 12 23881012 1.63E-06 1.63E-06
vg0800158999 sf0800157999 8 158999 1.78E-06 1.78E-06
vg0817500785 sf0817498071 8 17500785 1.86E-06 1.86E-06
vg1218155053 sf1218126489 12 18155053 2.41E-06 2.41E-06
vg1214331148 sf1214328488 12 14331148 2.62E-06 2.62E-06
vg1116613245 sf1116148123 11 16613245 2.95E-06 2.95E-06
vg1102781549 sf1102777453 11 2781549 3.63E-06 3.63E-06
vg0817461830 sf0817459116 8 17461830 4.92E-06 4.92E-06