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 mr1913 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
vg0406390054 sf0406385494 4 6390054 1.47E-44 7.21E-30
vg1122498353 sf1122032224 11 22498353 9.40E-15 8.40E-08
vg0912864929 sf0912863928 9 12864929 1.91E-14 1.81E-09
vg1004361310 sf1004377848 10 4361310 1.00E-13 2.15E-07
vg0817328107 sf0817325393 8 17328107 5.20E-13 1.68E-07
vg0406813538 sf0406808983 4 6813538 5.45E-11 2.88E-06
vg0406050134 sf0406045573 4 6050134 8.16E-11 3.37E-09
vg0912152486 sf0912151485 9 12152486 8.22E-10 5.50E-07
vg0823019901 sf0823017188 8 23019901 1.58E-09 3.17E-06
vg0614117993 sf0614116994 6 14117993 1.86E-09 2.23E-06
vg0431731747 sf0431546639 4 31731747 2.35E-09 1.15E-07
vg0714508778 sf0714507785 7 14508778 1.30E-08 1.90E-06
vg0912155913 sf0912154912 9 12155913 1.67E-08 4.54E-07
vg0234169418 sf0234163549 2 34169418 3.18E-08 1.42E-06
vg0622629240 sf0622628243 6 22629240 2.66E-07 7.44E-08
vg0819433740 sf0819431027 8 19433740 8.79E-07 2.01E-06
vg0207917838 sf0207917837 2 7917838 2.17E-06 6.10E-07
vg0417549349 sf0417377391 4 17549349 4.51E-06 2.89E-06
vg0406345590 sf0406341030 4 6345590 NA 1.53E-09
vg0720591049 sf0720590056 7 20591049 NA 2.71E-06