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 mr1449 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
vg0804848546 sf0804847549 8 4848546 1.20E-14 1.01E-06
vg0804847269 sf0804846272 8 4847269 5.45E-14 5.35E-07
vg0304638639 sf0304637641 3 4638639 2.22E-13 5.23E-06
vg0914372823 sf0914371822 9 14372823 3.11E-13 NA
vg0729650535 sf0729649543 7 29650535 6.19E-13 7.53E-06
vg1103070946 sf1103066850 11 3070946 6.21E-13 NA
vg0333461136 sf0333454006 3 33461136 7.32E-13 8.71E-07
vg0223395306 sf0223389437 2 23395306 1.87E-11 4.05E-06
vg0519281720 sf0519219204 5 19281720 4.37E-11 2.67E-06
vg0704180141 sf0704179142 7 4180141 7.67E-10 NA
vg0815904383 sf0815901669 8 15904383 1.55E-09 NA
vg0141817549 sf0141816506 1 41817549 7.20E-09 NA
vg0108804239 sf0108803239 1 8804239 NA 1.27E-07
vg0901601797 sf0901600797 9 1601797 NA 3.63E-07
vg0135050354 sf0135049311 1 35050354 NA 3.70E-06
vg1110012570 sf1110007147 11 10012570 NA 4.93E-06