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 mr1423 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
vg0216752678 sf0216746808 2 16752678 1.63E-24 1.26E-17
vg0217047369 sf0217041499 2 17047369 7.09E-24 7.07E-18
vg0216666516 sf0216660646 2 16666516 4.84E-12 6.89E-08
vg0217737908 sf0217732038 2 17737908 5.75E-12 2.83E-08
vg1217441137 sf1217435092 12 17441137 2.37E-11 1.09E-06
vg0213525745 sf0213525741 2 13525745 2.54E-11 3.21E-06
vg0217377905 sf0217372035 2 17377905 3.56E-11 2.53E-06
vg1210561587 sf1210559000 12 10561587 5.08E-10 6.93E-07
vg0217654127 sf0217648257 2 17654127 6.04E-10 2.37E-06
vg0218852605 sf0218846736 2 18852605 3.05E-08 1.76E-06
vg0216876069 sf0216870199 2 16876069 3.33E-07 9.25E-08
vg0820847989 sf0820845276 8 20847989 5.05E-07 1.75E-06
vg0525846261 sf0525783682 5 25846261 8.88E-07 2.66E-06
vg0719042389 sf0719041396 7 19042389 3.90E-06 5.11E-07
vg0116760985 sf0116759959 1 16760985 5.04E-06 7.58E-07
vg0226136784 sf0226130915 2 26136784 8.79E-06 NA
vg0404393344 sf0404388948 4 4393344 NA 1.22E-06