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 mr1535 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
vg1217066010 sf1217059965 12 17066010 4.32E-23 NA
vg0404341374 sf0404336979 4 4341374 7.85E-23 NA
vg0701923849 sf0701922850 7 1923849 7.46E-22 NA
vg0528026525 sf0527963880 5 28026525 4.51E-21 NA
vg0919812604 sf0919812123 9 19812604 6.51E-21 NA
vg0100676332 sf0100675332 1 676332 7.98E-17 NA
vg1020708879 sf1020637358 10 20708879 3.04E-15 7.86E-07
vg0420830218 sf0420658261 4 20830218 NA 9.82E-08
vg0420788121 sf0420616164 4 20788121 NA 2.46E-06
vg0520398639 sf0520336111 5 20398639 NA 2.52E-06
vg1003735124 sf1003734101 10 3735124 NA 2.87E-06
vg0803262517 sf0803261520 8 3262517 NA 3.20E-06
vg1119604110 sf1119137798 11 19604110 NA 3.97E-06
vg0520358656 sf0520296129 5 20358656 NA 9.23E-06