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 mr1129 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
vg0217047369 sf0217041499 2 17047369 6.61E-64 4.86E-37
vg0900337327 sf0900336327 9 337327 4.58E-23 4.50E-09
vg0900336799 sf0900335799 9 336799 1.35E-22 7.34E-10
vg0213525745 sf0213525741 2 13525745 3.95E-22 4.95E-08
vg0217137779 sf0217131909 2 17137779 2.24E-19 3.38E-07
vg0216357484 sf0216351614 2 16357484 8.54E-19 2.00E-10
vg0812023942 sf0812022947 8 12023942 4.15E-18 NA
vg0216278300 sf0216272430 2 16278300 4.26E-17 1.28E-07
vg1220237342 sf1220208784 12 20237342 1.24E-15 1.79E-06
vg0217737734 sf0217731864 2 17737734 1.38E-14 1.39E-08
vg0217861925 sf0217856056 2 17861925 2.62E-13 1.30E-06
vg0216594685 sf0216588815 2 16594685 3.75E-13 9.97E-09
vg0210804274 sf0210804272 2 10804274 2.60E-12 3.18E-06
vg1005364262 sf1005380799 10 5364262 1.91E-11 8.35E-08
vg0404016698 sf0404012305 4 4016698 7.02E-11 4.17E-06
vg0216876069 sf0216870199 2 16876069 2.46E-10 7.65E-09
vg0210480404 sf0210480402 2 10480404 2.73E-07 NA
vg0217296517 sf0217290647 2 17296517 NA 5.83E-07
vg0525571168 sf0525508589 5 25571168 NA 9.98E-07