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 mr1715 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
vg0308688680 sf0308687618 3 8688680 3.61E-28 NA
vg0727594847 sf0727593853 7 27594847 2.04E-27 NA
vg0140474219 sf0140473176 1 40474219 4.40E-27 NA
vg0406488877 sf0406484320 4 6488877 1.99E-25 NA
vg0234991023 sf0234985154 2 34991023 6.53E-25 NA
vg0719969117 sf0719968124 7 19969117 4.06E-21 7.24E-08
vg0726933455 sf0726932461 7 26933455 1.55E-19 NA
vg0526936018 sf0526873375 5 26936018 3.23E-18 1.16E-06
vg1126179996 sf1125708410 11 26179996 1.24E-17 4.69E-06
vg1101427839 sf1101426840 11 1427839 1.40E-17 2.38E-06
vg0305432173 sf0305431173 3 5432173 3.28E-17 NA
vg0122011942 sf0122010897 1 22011942 2.58E-16 1.81E-06
vg0129888300 sf0129887255 1 29888300 NA 1.10E-06
vg1003971250 sf1003970226 10 3971250 NA 2.82E-06
vg1126109948 sf1125638362 11 26109948 NA 3.64E-06
vg1225862443 sf1225828838 12 25862443 NA 3.93E-06
vg1225862470 sf1225828865 12 25862470 NA 4.34E-06
vg1019860440 sf1019788940 10 19860440 NA 4.69E-06