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 mr1132 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
vg1215968758 sf1215966054 12 15968758 6.38E-55 3.93E-28
vg1209571445 sf1209568854 12 9571445 1.59E-41 8.56E-18
vg1210709343 sf1210706756 12 10709343 2.67E-38 4.55E-18
vg1223872806 sf1223839259 12 23872806 2.01E-31 4.95E-08
vg1223873919 sf1223840372 12 23873919 1.17E-24 1.15E-06
vg1212938220 sf1212935559 12 12938220 1.43E-22 6.79E-10
vg1100960864 sf1100959865 11 960864 1.42E-19 1.77E-06
vg1101016914 sf1101015915 11 1016914 1.40E-18 6.33E-07
vg1223876846 sf1223843299 12 23876846 3.67E-17 2.08E-09
vg1215956423 sf1215953719 12 15956423 3.74E-15 3.48E-09
vg0217462843 sf0217456973 2 17462843 4.98E-15 1.78E-06
vg1217655012 sf1217648967 12 17655012 7.09E-15 6.20E-07
vg0315454216 sf0315452863 3 15454216 6.25E-14 1.10E-06
vg1215983666 sf1215980962 12 15983666 8.09E-14 1.17E-06
vg0526374490 sf0526311853 5 26374490 1.51E-13 2.18E-08
vg1216192507 sf1216189803 12 16192507 2.54E-13 4.61E-12
vg0317164649 sf0317163459 3 17164649 2.58E-13 1.48E-07
vg1207824599 sf1207822005 12 7824599 2.99E-12 1.23E-10
vg1215237966 sf1215235263 12 15237966 7.07E-12 3.96E-07
vg1210429306 sf1210426719 12 10429306 2.12E-10 2.06E-06
vg1220251034 sf1220222476 12 20251034 NA 9.37E-08
vg0706671410 sf0706670415 7 6671410 NA 5.45E-07
vg0624901622 sf0624900625 6 24901622 NA 6.31E-07
vg1209050414 sf1209047823 12 9050414 NA 2.05E-06