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 mr1738 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
vg0422162033 sf0421976914 4 22162033 5.13E-08 5.13E-08
vg0706405260 sf0706404265 7 6405260 1.25E-07 1.25E-07
vg0819484888 sf0819482175 8 19484888 3.10E-07 3.10E-07
vg0130239724 sf0130238679 1 30239724 3.54E-07 3.54E-07
vg0420711795 sf0420539838 4 20711795 5.44E-07 5.44E-07
vg0122971925 sf0122970881 1 22971925 6.49E-07 6.49E-07
vg0421384856 sf0421212909 4 21384856 8.94E-07 8.94E-07
vg1104467562 sf1104463464 11 4467562 9.79E-07 9.80E-07
vg0921004343 sf0921003862 9 21004343 1.44E-06 1.44E-06
vg0421220373 sf0421048425 4 21220373 1.64E-06 1.64E-06
vg0715502728 sf0715501735 7 15502728 2.44E-06 2.44E-06
vg0705692538 sf0705691539 7 5692538 2.49E-06 2.49E-06
vg0140684832 sf0140683789 1 40684832 2.83E-06 2.83E-06
vg0220791513 sf0220785645 2 20791513 3.88E-06 3.88E-06
vg0805826839 sf0805825842 8 5826839 4.30E-06 4.30E-06
vg1208280442 sf1208277848 12 8280442 4.40E-06 4.40E-06
vg0715369506 sf0715368513 7 15369506 4.40E-06 4.40E-06
vg0715311451 sf0715310458 7 15311451 4.41E-06 4.41E-06
vg0113601070 sf0113600044 1 13601070 4.74E-06 4.74E-06
vg0106635826 sf0106634826 1 6635826 7.37E-06 7.37E-06