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 mr1528 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
vg0716085095 sf0716084102 7 16085095 2.16E-14 3.64E-13
vg0716044467 sf0716043474 7 16044467 3.72E-14 1.17E-13
vg1101960971 sf1101959971 11 1960971 3.77E-12 NA
vg1102153486 sf1102149344 11 2153486 4.70E-11 3.96E-06
vg0827750460 sf0827747746 8 27750460 5.45E-11 NA
vg0134230502 sf0134229459 1 34230502 1.10E-10 NA
vg1207624027 sf1207621429 12 7624027 1.94E-10 NA
vg0716096216 sf0716095223 7 16096216 8.20E-08 3.47E-07
vg0400281402 sf0400292705 4 281402 9.93E-08 8.85E-07
vg1117585468 sf1117119325 11 17585468 9.95E-08 8.31E-07
vg0805947083 sf0805946086 8 5947083 2.08E-07 2.28E-07
vg0714880390 sf0714879397 7 14880390 3.55E-07 1.42E-06
vg0721652148 sf0721651155 7 21652148 5.63E-07 3.06E-06
vg0505638872 sf0505638810 5 5638872 8.60E-06 NA
vg0714860463 sf0714859470 7 14860463 NA 1.99E-08
vg0717047190 sf0717046197 7 17047190 NA 3.34E-07
vg0908678620 sf0908677619 9 8678620 NA 3.04E-06
vg1016562368 sf1016491141 10 16562368 NA 3.26E-06
vg0726216418 sf0726215424 7 26216418 NA 3.58E-06
vg1123663718 sf1123197588 11 23663718 NA 4.41E-06
vg0505638334 sf0505638272 5 5638334 NA 4.90E-06