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 mr1540 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
vg0122975265 sf0122974221 1 22975265 1.32E-22 NA
vg0520076406 sf0520013882 5 20076406 3.32E-22 NA
vg1000839305 sf1000838281 10 839305 8.77E-22 NA
vg0528181952 sf0528119307 5 28181952 1.07E-21 NA
vg1125433497 sf1124967336 11 25433497 4.25E-21 1.05E-07
vg0129933965 sf0129932920 1 29933965 1.91E-19 8.97E-07
vg1000448645 sf1000447621 10 448645 2.04E-19 NA
vg0132750478 sf0132749434 1 32750478 5.05E-16 2.53E-06
vg0103174854 sf0103173854 1 3174854 1.13E-15 4.51E-06
vg0129868849 sf0129867804 1 29868849 1.65E-15 4.05E-08
vg1016384387 sf1016313163 10 16384387 1.95E-14 4.77E-06
vg1016929873 sf1016858645 10 16929873 2.61E-14 7.54E-08
vg1125475428 sf1125009267 11 25475428 3.53E-14 3.21E-09
vg0314829204 sf0314827851 3 14829204 6.72E-14 3.18E-07
vg1122054372 sf1121588243 11 22054372 1.25E-13 4.23E-06
vg0110837074 sf0110836050 1 10837074 1.81E-13 8.78E-07
vg0312540667 sf0312539385 3 12540667 4.61E-13 6.52E-07
vg0520368088 sf0520305561 5 20368088 1.10E-12 2.45E-06
vg1127574591 sf1127102978 11 27574591 NA 1.24E-08
vg0713262354 sf0713261361 7 13262354 NA 2.62E-07
vg1214642525 sf1214639865 12 14642525 NA 7.31E-07
vg1214645996 sf1214643336 12 14645996 NA 8.25E-07
vg1003063551 sf1003062528 10 3063551 NA 1.64E-06
vg0104000364 sf0103999364 1 4000364 NA 4.08E-06
vg0818704582 sf0818701869 8 18704582 NA 4.08E-06
vg1119446199 sf1118979887 11 19446199 NA 4.15E-06
vg0801145104 sf0801144106 8 1145104 NA 4.82E-06
vg0122690936 sf0122689891 1 22690936 NA 5.24E-06