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 mr1904 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
vg1102066617 sf1102062475 11 2066617 1.03E-23 2.27E-10
vg1102045515 sf1102041373 11 2045515 1.06E-23 1.95E-10
vg1102069737 sf1102065595 11 2069737 1.46E-23 2.37E-10
vg0424118771 sf0423933632 4 24118771 9.50E-15 NA
vg0507018740 sf0507018682 5 7018740 1.09E-14 NA
vg0105385381 sf0105384381 1 5385381 4.08E-14 NA
vg1122523293 sf1122057164 11 22523293 4.86E-14 NA
vg0107213426 sf0107212426 1 7213426 8.15E-13 2.60E-06
vg0103794839 sf0103793839 1 3794839 2.85E-10 NA
vg1102068403 sf1102064261 11 2068403 NA 8.66E-09
vg0116970135 sf0116969089 1 16970135 NA 1.82E-06
vg1114877180 sf1114413494 11 14877180 NA 2.10E-06
vg0714702171 sf0714701178 7 14702171 NA 2.70E-06
vg1001638642 sf1001637619 10 1638642 NA 2.74E-06
vg1115069932 sf1114606246 11 15069932 NA 4.64E-06
vg0515921851 sf0515864358 5 15921851 NA 4.65E-06
vg0412453374 sf0412444089 4 12453374 NA 4.84E-06
vg0710590918 sf0710589924 7 10590918 NA 7.81E-06