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 mr1748 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
vg0908324423 sf0908323423 9 8324423 1.25E-08 2.39E-06
vg0140366212 sf0140365169 1 40366212 3.62E-08 NA
vg0419536798 sf0419364836 4 19536798 5.58E-08 1.38E-06
vg0412333059 sf0412323774 4 12333059 9.20E-08 NA
vg1126333420 sf1125861833 11 26333420 9.32E-08 NA
vg0209662259 sf0209662257 2 9662259 4.91E-07 7.08E-08
vg0417758175 sf0417586212 4 17758175 3.27E-06 3.08E-06
vg0208439342 sf0208439341 2 8439342 3.96E-06 1.33E-06
vg1012629654 sf1012558469 10 12629654 5.52E-06 1.76E-06
vg0208637781 sf0208637780 2 8637781 6.93E-06 3.08E-06
vg1122649502 sf1122183373 11 22649502 6.94E-06 1.87E-07
vg0705673479 sf0705672480 7 5673479 NA 4.56E-08
vg0331686127 sf0331679004 3 31686127 NA 1.29E-07
vg0141120189 sf0141119146 1 41120189 NA 1.07E-06
vg1119170143 sf1118703831 11 19170143 NA 3.58E-06
vg0922001438 sf0922000957 9 22001438 NA 4.18E-06