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 mr1383 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
vg0224040800 sf0224034931 2 24040800 4.70E-25 NA
vg0224067817 sf0224061948 2 24067817 3.94E-24 4.96E-06
vg0206158957 sf0206158957 2 6158957 4.04E-24 NA
vg0141212628 sf0141211585 1 41212628 6.50E-24 NA
vg1016847259 sf1016776031 10 16847259 1.34E-23 NA
vg0807552457 sf0807551462 8 7552457 2.95E-23 NA
vg1000080974 sf1000079974 10 80974 1.85E-22 6.00E-08
vg1016854726 sf1016783498 10 16854726 3.54E-22 NA
vg0140619974 sf0140618931 1 40619974 7.56E-22 NA
vg0140492713 sf0140491670 1 40492713 7.39E-21 NA
vg1219966213 sf1219937683 12 19966213 1.17E-18 2.35E-06
vg1000079710 sf1000078710 10 79710 NA 2.74E-08
vg0700016817 sf0700015817 7 16817 NA 2.79E-08
vg0700008597 sf0700007597 7 8597 NA 2.84E-07
vg0134784290 sf0134783247 1 34784290 NA 2.94E-07
vg0119738433 sf0119737388 1 19738433 NA 5.69E-07
vg0303236377 sf0303235373 3 3236377 NA 6.96E-07
vg1021218403 sf1021146881 10 21218403 NA 7.90E-07
vg0700333296 sf0700332296 7 333296 NA 3.03E-06