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 mr1213 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
vg0719090536 sf0719089543 7 19090536 6.99E-51 6.88E-28
vg0705758057 sf0705757058 7 5758057 8.91E-17 7.64E-07
vg0719100537 sf0719099544 7 19100537 4.79E-16 1.82E-09
vg0335407181 sf0335400050 3 35407181 2.36E-15 NA
vg0719448599 sf0719447606 7 19448599 1.74E-14 5.30E-11
vg0705751437 sf0705750438 7 5751437 2.31E-14 1.77E-07
vg0336379800 sf0336372670 3 36379800 6.29E-13 4.20E-08
vg0719155559 sf0719154566 7 19155559 5.19E-12 2.24E-10
vg0706009335 sf0706008336 7 6009335 6.29E-12 1.43E-06
vg0235249589 sf0235243720 2 35249589 8.61E-12 3.52E-06
vg0900606284 sf0900605284 9 606284 9.06E-12 1.55E-07
vg0431283538 sf0431098428 4 31283538 1.16E-11 NA
vg0431597089 sf0431411984 4 31597089 3.71E-11 4.32E-06
vg0402208784 sf0402204379 4 2208784 7.76E-11 2.16E-06
vg0719120986 sf0719119993 7 19120986 7.41E-10 5.75E-10
vg0228211458 sf0228205589 2 28211458 4.38E-09 9.81E-07
vg0718984580 sf0718983587 7 18984580 5.21E-09 6.13E-10
vg1202108891 sf1202107889 12 2108891 NA 2.24E-06
vg1017014524 sf1016943296 10 17014524 NA 2.36E-06