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 mr1993 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
vg0417021326 sf0416849368 4 17021326 1.12E-18 2.89E-07
vg0417121176 sf0416949218 4 17121176 1.97E-18 6.53E-09
vg0915125886 sf0915124885 9 15125886 6.03E-17 NA
vg0905616909 sf0905615909 9 5616909 9.65E-17 4.40E-06
vg0401797174 sf0401792769 4 1797174 1.53E-16 NA
vg0410354028 sf0410344727 4 10354028 1.55E-16 5.37E-06
vg0111193660 sf0111192636 1 11193660 4.81E-15 1.29E-07
vg1227225152 sf1227191552 12 27225152 6.12E-15 4.42E-07
vg0717573276 sf0717572283 7 17573276 6.46E-14 4.50E-06
vg0810074467 sf0810073471 8 10074467 8.54E-14 3.02E-07
vg0720597910 sf0720596917 7 20597910 1.20E-13 7.03E-08
vg0403055424 sf0403051028 4 3055424 1.33E-13 2.48E-06
vg0601799907 sf0601798908 6 1799907 5.20E-12 4.87E-06
vg0817973700 sf0817970987 8 17973700 5.62E-12 3.97E-07
vg0704818663 sf0704817664 7 4818663 NA 1.07E-07
vg0406376847 sf0406372287 4 6376847 NA 4.89E-07
vg0417407132 sf0417235175 4 17407132 NA 4.97E-07
vg0417992105 sf0417820146 4 17992105 NA 6.15E-07
vg0608163436 sf0608162437 6 8163436 NA 7.60E-07
vg1126758736 sf1126287123 11 26758736 NA 1.09E-06
vg0101880727 sf0101879727 1 1880727 NA 1.53E-06
vg0627547379 sf0627546381 6 27547379 NA 1.58E-06
vg0806250261 sf0806249266 8 6250261 NA 2.37E-06
vg0228455926 sf0228450057 2 28455926 NA 2.39E-06
vg0816453653 sf0816450939 8 16453653 NA 2.77E-06