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 mr1349 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
vg1006619818 sf1006635441 10 6619818 8.14E-09 8.14E-09
vg0506942442 sf0506942384 5 6942442 3.79E-07 3.79E-07
vg1206532904 sf1206531794 12 6532904 8.36E-07 8.36E-07
vg1000994377 sf1000993353 10 994377 9.54E-07 9.54E-07
vg0118364509 sf0118363463 1 18364509 1.01E-06 1.01E-06
vg0909772073 sf0909771072 9 9772073 1.12E-06 1.12E-06
vg1227262581 sf1227228981 12 27262581 1.44E-06 1.44E-06
vg1114474967 sf1114011284 11 14474967 2.97E-06 2.97E-06
vg1208535416 sf1208532823 12 8535416 3.02E-06 3.02E-06
vg0114830962 sf0114829936 1 14830962 4.27E-06 4.27E-06
vg1218127830 sf1218099266 12 18127830 4.84E-06 4.84E-06
vg0805498945 sf0805497948 8 5498945 6.14E-06 6.14E-06