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 mr1900 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
vg1124986395 sf1124520235 11 24986395 4.82E-48 8.92E-35
vg1125432444 sf1124966283 11 25432444 2.50E-26 1.77E-11
vg1015670808 sf1015599578 10 15670808 3.10E-25 4.63E-08
vg0105168999 sf0105167999 1 5168999 3.30E-25 4.02E-07
vg1124875808 sf1124409648 11 24875808 5.08E-25 6.59E-21
vg1125024893 sf1124558733 11 25024893 1.69E-24 1.38E-11
vg0812591477 sf0812589302 8 12591477 1.13E-21 4.60E-08
vg1125042652 sf1124576492 11 25042652 2.15E-20 9.38E-18
vg1122492947 sf1122026818 11 22492947 6.64E-20 1.54E-08
vg1125037808 sf1124571648 11 25037808 NA 1.51E-18
vg1124931687 sf1124465527 11 24931687 NA 1.49E-14
vg1125080303 sf1124614143 11 25080303 NA 4.61E-12
vg1125089512 sf1124623352 11 25089512 NA 6.67E-12
vg0328637867 sf0328630920 3 28637867 NA 8.81E-12
vg1124988847 sf1124522687 11 24988847 NA 5.26E-11
vg1124320687 sf1123854557 11 24320687 NA 1.62E-09
vg0717185752 sf0717184759 7 17185752 NA 2.37E-09
vg1125113751 sf1124647591 11 25113751 NA 2.71E-09
vg1125441578 sf1124975417 11 25441578 NA 6.77E-09
vg1125091275 sf1124625115 11 25091275 NA 1.01E-08
vg1125079769 sf1124613609 11 25079769 NA 2.45E-08
vg1118023722 sf1117557580 11 18023722 NA 2.70E-08
vg0621172424 sf0621171427 6 21172424 NA 3.27E-08
vg0307571121 sf0307570059 3 7571121 NA 5.85E-08
vg1124992937 sf1124526777 11 24992937 NA 4.75E-07