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 mr1159 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
vg0726559146 sf0726558152 7 26559146 5.43E-10 1.16E-07
vg1118177146 sf1117711004 11 18177146 8.99E-10 NA
vg0919409649 sf0919409239 9 19409649 6.37E-09 NA
vg0131768442 sf0131767398 1 31768442 6.99E-09 NA
vg0527921996 sf0527859353 5 27921996 1.32E-08 NA
vg0517977755 sf0517917241 5 17977755 4.17E-08 3.07E-06
vg0528836237 sf0528773592 5 28836237 1.59E-07 6.43E-08
vg1212024054 sf1212021389 12 12024054 2.08E-07 4.52E-07
vg0811404383 sf0811403388 8 11404383 1.09E-06 4.72E-06
vg0126514398 sf0126513354 1 26514398 6.78E-06 3.58E-07
vg0335297514 sf0335290383 3 35297514 7.37E-06 2.14E-06
vg0801628860 sf0801627862 8 1628860 NA 4.67E-07
vg0715152264 sf0715151271 7 15152264 NA 2.40E-06
vg1020531763 sf1020460242 10 20531763 NA 4.84E-06