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 mr1172 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
vg0421272904 sf0421100958 4 21272904 3.64E-14 NA
vg0210463160 sf0210463158 2 10463160 4.17E-14 2.37E-09
vg0725489607 sf0725488613 7 25489607 8.17E-13 NA
vg0907342967 sf0907341967 9 7342967 8.45E-13 9.09E-11
vg1200672282 sf1200671282 12 672282 3.27E-12 NA
vg0219643578 sf0219637710 2 19643578 5.55E-12 7.36E-07
vg0909046504 sf0909045503 9 9046504 6.71E-12 1.19E-08
vg0406825130 sf0406820575 4 6825130 1.86E-11 3.53E-07
vg1210359727 sf1210357140 12 10359727 8.70E-11 1.73E-07
vg0608024130 sf0608023131 6 8024130 1.95E-10 NA
vg0433300288 sf0433115176 4 33300288 3.11E-10 1.25E-07
vg0217718819 sf0217712949 2 17718819 4.96E-10 2.83E-06
vg0405740895 sf0405736334 4 5740895 6.88E-10 4.91E-08
vg1114292062 sf1113828383 11 14292062 8.80E-10 2.08E-07
vg0412733978 sf0412724688 4 12733978 1.57E-09 1.45E-06
vg0819068739 sf0819066026 8 19068739 1.70E-09 6.17E-09
vg0907333374 sf0907332374 9 7333374 2.45E-09 1.29E-07
vg0104472462 sf0104471462 1 4472462 7.09E-09 1.71E-06
vg0226419846 sf0226413977 2 26419846 9.94E-09 1.94E-07
vg0120873100 sf0120872055 1 20873100 1.09E-08 1.71E-06
vg0420090563 sf0419918599 4 20090563 1.37E-08 NA
vg1022802911 sf1022731384 10 22802911 1.64E-08 2.27E-06
vg0211446231 sf0211446227 2 11446231 1.66E-08 NA
vg0141145804 sf0141144761 1 41145804 NA 4.04E-07
vg0220182817 sf0220176949 2 20182817 NA 4.73E-07
vg1000966667 sf1000965643 10 966667 NA 5.53E-07
vg0808455943 sf0808454947 8 8455943 NA 8.71E-07
vg0220188422 sf0220182554 2 20188422 NA 9.79E-07
vg1219197044 sf1219168514 12 19197044 NA 2.50E-06
vg0401643541 sf0401639090 4 1643541 NA 2.63E-06