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 mr1071 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 1.62E-16 3.58E-12
vg0406944063 sf0406939331 4 6944063 3.29E-15 1.00E-11
vg0616169045 sf0616168047 6 16169045 2.58E-10 6.87E-07
vg0406592386 sf0406587830 4 6592386 2.84E-10 8.33E-09
vg0412100387 sf0412091098 4 12100387 4.97E-10 2.86E-07
vg0224622358 sf0224616489 2 24622358 5.79E-10 NA
vg0616244147 sf0616243149 6 16244147 1.53E-09 2.20E-09
vg1205463941 sf1205462927 12 5463941 4.55E-09 1.54E-06
vg0407665649 sf0407660916 4 7665649 3.01E-08 4.23E-11
vg0406633967 sf0406629411 4 6633967 3.39E-08 1.71E-06
vg0618618072 sf0618617075 6 18618072 3.63E-08 2.37E-07
vg0406862446 sf0406857891 4 6862446 7.79E-08 2.56E-07
vg0406944392 sf0406939660 4 6944392 8.07E-08 2.05E-06
vg1218763524 sf1218734959 12 18763524 8.80E-08 1.07E-07
vg1202580538 sf1202579540 12 2580538 1.21E-07 1.80E-06
vg0412128903 sf0412119614 4 12128903 1.54E-07 1.07E-06
vg0418306299 sf0418134346 4 18306299 3.43E-07 5.16E-07
vg0112215171 sf0112214145 1 12215171 6.20E-07 1.56E-06
vg0614933791 sf0614932792 6 14933791 1.19E-06 1.88E-06
vg0514203146 sf0514145689 5 14203146 1.95E-06 NA
vg1210467503 sf1210464916 12 10467503 2.14E-06 4.84E-09
vg1202576537 sf1202575539 12 2576537 3.61E-06 NA
vg0226252166 sf0226246297 2 26252166 4.49E-06 NA
vg0412466084 sf0412456799 4 12466084 5.12E-06 NA
vg1226826332 sf1226792731 12 26826332 NA 7.17E-07
vg0217616525 sf0217610655 2 17616525 NA 1.39E-06
vg0715307926 sf0715306933 7 15307926 NA 2.37E-06
vg0409567751 sf0409558449 4 9567751 NA 5.65E-06