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 mr1549 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
vg0709261513 sf0709260519 7 9261513 1.46E-15 NA
vg0709269240 sf0709268246 7 9269240 1.85E-15 2.63E-06
vg0414201150 sf0414191866 4 14201150 1.07E-13 6.91E-06
vg1000204921 sf1000203921 10 204921 6.27E-13 NA
vg0501517057 sf0501517041 5 1517057 2.05E-12 NA
vg0417122308 sf0416950350 4 17122308 2.05E-12 9.53E-06
vg0419005856 sf0418833898 4 19005856 1.60E-11 5.07E-09
vg0209688142 sf0209688140 2 9688142 5.90E-11 1.13E-08
vg0218470342 sf0218464473 2 18470342 1.01E-10 NA
vg1000636049 sf1000635025 10 636049 1.45E-10 1.25E-06
vg0401895649 sf0401891245 4 1895649 1.54E-10 NA
vg1020589936 sf1020518415 10 20589936 1.88E-10 1.98E-07
vg0920454686 sf0920454205 9 20454686 1.98E-10 1.65E-07
vg0713017347 sf0713016354 7 13017347 5.12E-10 NA
vg0728945909 sf0728944917 7 28945909 7.97E-09 1.18E-07
vg0402346536 sf0402342131 4 2346536 1.99E-08 5.91E-07
vg1003873169 sf1003872145 10 3873169 2.35E-08 NA
vg1202415264 sf1202414265 12 2415264 NA 4.26E-10
vg0412080354 sf0412071065 4 12080354 NA 7.36E-07
vg0621414627 sf0621413630 6 21414627 NA 7.77E-07
vg0411852309 sf0411843020 4 11852309 NA 1.43E-06
vg0617983870 sf0617982873 6 17983870 NA 1.65E-06
vg0404582911 sf0404578514 4 4582911 NA 2.50E-06
vg0416659011 sf0416487051 4 16659011 NA 2.73E-06
vg0108564628 sf0108563628 1 8564628 NA 3.00E-06
vg0804127081 sf0804126084 8 4127081 NA 3.20E-06
vg0412663837 sf0412654547 4 12663837 NA 3.88E-06
vg1000604296 sf1000603272 10 604296 NA 3.92E-06
vg0333362258 sf0333355128 3 33362258 NA 4.42E-06