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 mr1082 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
vg0719064221 sf0719063228 7 19064221 4.45E-45 1.65E-32
vg0719049906 sf0719048913 7 19049906 9.31E-45 6.82E-33
vg0626833038 sf0626832041 6 26833038 2.11E-40 1.49E-10
vg0304920390 sf0304919392 3 4920390 2.45E-40 2.62E-06
vg0608380194 sf0608379195 6 8380194 4.54E-40 NA
vg0706739769 sf0706738774 7 6739769 9.67E-40 4.69E-06
vg0719091461 sf0719090468 7 19091461 NA 6.00E-23
vg0719151972 sf0719150979 7 19151972 NA 1.35E-22
vg0719065396 sf0719064403 7 19065396 NA 2.28E-22
vg0719141601 sf0719140608 7 19141601 NA 3.35E-22
vg0719145724 sf0719144731 7 19145724 NA 2.47E-20
vg0707667722 sf0707666727 7 7667722 NA 1.30E-15
vg0719436399 sf0719435406 7 19436399 NA 5.45E-14
vg0113087370 sf0113086344 1 13087370 NA 8.06E-12
vg0719466615 sf0719465622 7 19466615 NA 9.99E-12
vg0130667376 sf0130666332 1 30667376 NA 5.43E-11
vg0325018273 sf0325016353 3 25018273 NA 8.96E-10
vg0704871363 sf0704870364 7 4871363 NA 9.49E-10
vg0608463867 sf0608462868 6 8463867 NA 1.01E-09
vg0616961888 sf0616960891 6 16961888 NA 1.12E-09
vg0620151422 sf0620150425 6 20151422 NA 1.29E-09
vg0704482336 sf0704481337 7 4482336 NA 1.80E-09
vg0302596616 sf0302595612 3 2596616 NA 4.02E-09
vg0719618102 sf0719617109 7 19618102 NA 5.09E-09
vg1110835875 sf1110830192 11 10835875 NA 6.78E-09
vg0626891249 sf0626890252 6 26891249 NA 6.85E-09
vg0130826614 sf0130825570 1 30826614 NA 8.63E-09
vg0709019375 sf0709018381 7 9019375 NA 9.04E-09
vg0112972548 sf0112971522 1 12972548 NA 6.61E-06