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 mr1751 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
vg0805724088 sf0805723091 8 5724088 1.20E-14 NA
vg0725460660 sf0725459666 7 25460660 1.24E-14 NA
vg0500589004 sf0500589004 5 589004 5.99E-14 NA
vg0623460564 sf0623459567 6 23460564 1.16E-13 NA
vg0912892254 sf0912891253 9 12892254 1.44E-13 NA
vg0717527954 sf0717526961 7 17527954 2.18E-13 1.93E-06
vg0501783564 sf0501783547 5 1783564 9.54E-13 3.48E-07
vg0318955179 sf0318953939 3 18955179 1.06E-12 NA
vg1100571681 sf1100570684 11 571681 8.77E-12 3.85E-06
vg0401963741 sf0401959337 4 1963741 NA 9.61E-07
vg1002298537 sf1002297514 10 2298537 NA 1.25E-06