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 mr1373 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
vg1103158490 sf1103154393 11 3158490 3.91E-10 2.75E-07
vg0819985304 sf0819982591 8 19985304 2.27E-09 1.27E-06
vg0717128012 sf0717127019 7 17128012 2.14E-08 2.23E-07
vg0420718113 sf0420546156 4 20718113 4.20E-08 1.21E-07
vg1000961132 sf1000960108 10 961132 5.24E-08 NA
vg1215307750 sf1215305048 12 15307750 8.07E-08 2.46E-07
vg0817557507 sf0817554793 8 17557507 2.13E-07 6.68E-07
vg0325188819 sf0325186900 3 25188819 2.17E-07 2.08E-06
vg0200521736 sf0200521736 2 521736 4.33E-07 8.33E-08
vg0516302066 sf0516244548 5 16302066 5.01E-07 3.39E-06
vg0607692076 sf0607691077 6 7692076 6.64E-07 3.48E-06
vg0105393860 sf0105392860 1 5393860 4.11E-06 4.69E-07
vg0113600896 sf0113599870 1 13600896 4.24E-06 4.14E-06
vg1000702985 sf1000701961 10 702985 4.39E-06 1.89E-06
vg1000501145 sf1000500121 10 501145 9.75E-06 4.27E-06
vg0510460804 sf0510460733 5 10460804 NA 8.93E-07
vg0421318693 sf0421146747 4 21318693 NA 1.71E-06
vg0229409337 sf0229403468 2 29409337 NA 4.76E-06