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 mr1113 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
vg1203346568 sf1203345571 12 3346568 6.00E-15 1.82E-09
vg1203128564 sf1203127567 12 3128564 1.50E-14 3.27E-10
vg0728158141 sf0728157148 7 28158141 4.72E-14 2.96E-10
vg0421387824 sf0421215877 4 21387824 6.82E-14 1.14E-10
vg0315684189 sf0315682836 3 15684189 1.88E-13 5.18E-10
vg0222717674 sf0222711805 2 22717674 2.11E-13 4.39E-10
vg0918474400 sf0918473399 9 18474400 5.50E-13 2.06E-11
vg0516420381 sf0516362863 5 16420381 1.12E-12 6.45E-08
vg0231678187 sf0231672318 2 31678187 6.92E-12 3.20E-09
vg0336193973 sf0336186899 3 36193973 7.61E-12 1.19E-08
vg0714344926 sf0714343933 7 14344926 1.30E-10 4.03E-08
vg0625443240 sf0625442243 6 25443240 3.89E-10 1.31E-07
vg0435094145 sf0434909034 4 35094145 6.54E-10 1.65E-08
vg1216556661 sf1216553954 12 16556661 8.94E-10 1.49E-07
vg1119545646 sf1119079334 11 19545646 1.04E-09 1.42E-08
vg1117137503 sf1116671355 11 17137503 1.29E-09 4.14E-08
vg0818709501 sf0818706788 8 18709501 5.08E-09 3.80E-08
vg0133772255 sf0133771211 1 33772255 9.59E-09 1.11E-08
vg0122011839 sf0122010794 1 22011839 1.32E-08 2.49E-07
vg0122754153 sf0122753109 1 22754153 1.70E-08 5.55E-08
vg0805024504 sf0805023507 8 5024504 5.74E-06 2.72E-07