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 mr1235 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
vg0216752678 sf0216746808 2 16752678 4.19E-25 2.82E-15
vg0217047369 sf0217041499 2 17047369 9.34E-25 1.25E-15
vg1210426367 sf1210423780 12 10426367 4.21E-17 3.39E-07
vg0217232499 sf0217226629 2 17232499 3.14E-16 4.32E-06
vg1217425882 sf1217419837 12 17425882 1.54E-15 NA
vg0216888886 sf0216883016 2 16888886 1.89E-15 5.45E-08
vg0216755732 sf0216749862 2 16755732 2.24E-15 4.58E-07
vg1217440211 sf1217434166 12 17440211 1.13E-14 1.81E-06
vg0216666516 sf0216660646 2 16666516 8.29E-14 3.66E-07
vg0216644210 sf0216638340 2 16644210 2.23E-13 1.58E-06
vg0217654127 sf0217648257 2 17654127 2.35E-13 2.37E-06
vg1210331374 sf1210328787 12 10331374 2.60E-13 3.10E-07
vg0213525745 sf0213525741 2 13525745 1.09E-12 4.24E-06
vg0217737908 sf0217732038 2 17737908 5.01E-12 3.24E-06
vg1217929894 sf1217901328 12 17929894 2.78E-10 1.00E-06
vg0906503065 sf0906502065 9 6503065 1.12E-07 8.47E-06
vg0526012382 sf0525949802 5 26012382 NA 2.28E-06
vg0404393344 sf0404388948 4 4393344 NA 2.96E-06
vg0411806765 sf0411797476 4 11806765 NA 3.18E-06
vg0514024444 sf0513966988 5 14024444 NA 4.95E-06