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 mr1832 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
vg0420711795 sf0420539838 4 20711795 1.27E-08 1.27E-08
vg0122971925 sf0122970881 1 22971925 2.18E-08 2.19E-08
vg0819451071 sf0819448358 8 19451071 1.08E-07 1.08E-07
vg0717084739 sf0717083746 7 17084739 1.97E-07 1.97E-07
vg0921004343 sf0921003862 9 21004343 2.49E-07 2.49E-07
vg0424181194 sf0423996055 4 24181194 7.62E-07 7.63E-07
vg1104467562 sf1104463464 11 4467562 9.65E-07 9.66E-07
vg0817327549 sf0817324835 8 17327549 1.08E-06 1.08E-06
vg1104596684 sf1104592586 11 4596684 1.18E-06 1.18E-06
vg0411938695 sf0411929406 4 11938695 1.19E-06 1.19E-06
vg0715502728 sf0715501735 7 15502728 1.19E-06 1.20E-06
vg1215307750 sf1215305048 12 15307750 1.61E-06 1.61E-06
vg0706405260 sf0706404265 7 6405260 1.72E-06 1.72E-06
vg0623981969 sf0623980972 6 23981969 1.75E-06 1.75E-06
vg0805826839 sf0805825842 8 5826839 1.93E-06 1.93E-06
vg0316786845 sf0316785719 3 16786845 2.00E-06 2.00E-06
vg0131779655 sf0131778611 1 31779655 2.03E-06 2.03E-06
vg1226936545 sf1226902944 12 26936545 2.24E-06 2.24E-06
vg0620734924 sf0620733927 6 20734924 2.34E-06 2.34E-06
vg0714877053 sf0714876060 7 14877053 2.89E-06 2.89E-06