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
vg1124468452 sf1124002292 11 24468452 1.13E-11 1.13E-11
vg0812679480 sf0812677305 8 12679480 3.54E-11 3.54E-11
vg0805902939 sf0805901942 8 5902939 5.03E-10 5.03E-10
vg0620312022 sf0620311025 6 20312022 8.72E-10 8.73E-10
vg0713136981 sf0713135988 7 13136981 9.07E-10 9.07E-10
vg0521870267 sf0521807709 5 21870267 2.05E-09 2.05E-09
vg1104422091 sf1104417993 11 4422091 2.06E-09 2.06E-09
vg0319387507 sf0319386018 3 19387507 4.98E-09 4.98E-09
vg0407782510 sf0407777778 4 7782510 1.66E-08 1.66E-08
vg0221902760 sf0221896891 2 21902760 2.39E-08 2.39E-08
vg0113027104 sf0113026078 1 13027104 5.44E-08 5.44E-08
vg0410375848 sf0410366547 4 10375848 7.36E-08 7.37E-08
vg1124965681 sf1124499521 11 24965681 9.57E-08 9.57E-08
vg0525249866 sf0525187287 5 25249866 1.61E-07 1.61E-07
vg1106643219 sf1106638972 11 6643219 2.80E-07 2.80E-07
vg0811941721 sf0811940726 8 11941721 2.81E-07 2.81E-07
vg0205996999 sf0205996999 2 5996999 3.02E-07 3.02E-07
vg0301364612 sf0301363610 3 1364612 3.08E-07 3.08E-07
vg0521578860 sf0521511524 5 21578860 3.23E-07 3.23E-07
vg0809872000 sf0809871004 8 9872000 3.76E-07 3.76E-07