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 mr1962 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
vg0406562314 sf0406557757 4 6562314 3.17E-18 2.02E-15
vg0406097513 sf0406092952 4 6097513 1.55E-16 1.26E-13
vg1016228574 sf1016157346 10 16228574 7.41E-10 6.05E-07
vg0614107939 sf0614106940 6 14107939 1.94E-09 8.65E-11
vg0712115727 sf0712114733 7 12115727 6.21E-09 9.67E-08
vg0807117547 sf0807116552 8 7117547 8.62E-09 8.54E-08
vg0916688695 sf0916687694 9 16688695 9.29E-09 1.60E-07
vg0202518756 sf0202518754 2 2518756 1.40E-08 1.42E-08
vg0712115543 sf0712114549 7 12115543 1.40E-08 7.41E-08
vg0705940927 sf0705939928 7 5940927 1.96E-08 9.74E-07
vg0430673937 sf0430488812 4 30673937 2.48E-08 2.38E-08
vg1017720440 sf1017649213 10 17720440 2.90E-08 6.09E-08
vg0124173863 sf0124172819 1 24173863 3.59E-08 4.63E-07
vg0432345183 sf0432160072 4 32345183 5.95E-08 1.39E-08
vg1004594577 sf1004611115 10 4594577 6.18E-08 6.28E-07
vg1206256269 sf1206255159 12 6256269 4.39E-07 1.52E-07
vg1209921454 sf1209918864 12 9921454 4.49E-07 2.85E-07
vg0209656030 sf0209656028 2 9656030 1.24E-06 5.56E-07
vg1128763670 sf1128240449 11 28763670 1.67E-06 6.91E-07
vg1118025749 sf1117559607 11 18025749 1.68E-06 4.72E-07
vg1128773900 sf1128250679 11 28773900 6.22E-06 1.34E-07
vg0311534838 sf0311533556 3 11534838 NA 1.50E-06