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 mr1771 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
vg1018891503 sf1018820059 10 18891503 5.41E-16 8.02E-07
vg1019101727 sf1019030284 10 19101727 6.07E-16 7.94E-08
vg0434375534 sf0434190428 4 34375534 7.32E-14 7.22E-06
vg1219345800 sf1219317270 12 19345800 3.02E-13 NA
vg0810459509 sf0810458513 8 10459509 1.13E-12 NA
vg0816042103 sf0816039389 8 16042103 1.39E-12 NA
vg1200274541 sf1200273541 12 274541 2.52E-12 3.24E-06
vg0231389934 sf0231384065 2 31389934 4.53E-12 2.90E-07
vg0406525139 sf0406520582 4 6525139 8.98E-12 5.40E-07
vg0700837076 sf0700836076 7 837076 4.07E-10 2.22E-06
vg0432523918 sf0432338810 4 32523918 NA 4.62E-07