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 mr1662 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
vg1125476275 sf1125010114 11 25476275 7.11E-22 3.56E-17
vg1125514201 sf1125048040 11 25514201 1.03E-14 2.37E-10
vg1125521509 sf1125055348 11 25521509 3.36E-14 1.40E-10
vg0713261078 sf0713260085 7 13261078 5.26E-12 1.52E-07
vg1128772910 sf1128249689 11 28772910 2.69E-11 6.19E-07
vg1126936113 sf1126464500 11 26936113 3.65E-11 4.50E-07
vg0507714473 sf0507714414 5 7714473 1.63E-10 3.82E-07
vg1126344683 sf1125873096 11 26344683 9.12E-10 4.44E-08
vg1125471041 sf1125004880 11 25471041 1.09E-09 9.37E-10
vg1126423874 sf1125952287 11 26423874 1.52E-09 6.84E-08
vg1226691637 sf1226658033 12 26691637 2.21E-09 NA
vg1125621218 sf1125155057 11 25621218 3.95E-09 1.49E-07
vg1128708282 sf1128185061 11 28708282 5.49E-09 1.33E-06
vg1125473544 sf1125007383 11 25473544 7.06E-09 4.61E-09
vg1125256440 sf1124790280 11 25256440 7.52E-09 4.65E-06
vg0713264535 sf0713263542 7 13264535 1.07E-07 1.82E-06
vg1126329129 sf1125857542 11 26329129 1.31E-07 1.87E-06
vg1125392771 sf1124926610 11 25392771 3.75E-07 1.72E-06
vg1125615015 sf1125148854 11 25615015 1.07E-06 3.01E-06
vg0100479137 sf0100478137 1 479137 1.55E-06 NA
vg1129015783 sf1128492562 11 29015783 5.49E-06 6.79E-07
vg1125228571 sf1124762411 11 25228571 NA 3.78E-08
vg1125820968 sf1125354887 11 25820968 NA 7.17E-07
vg0709176888 sf0709175894 7 9176888 NA 8.91E-07
vg1125419021 sf1124952860 11 25419021 NA 4.92E-06