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 mr1200 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
vg0610480621 sf0610479622 6 10480621 7.55E-101 4.85E-30
vg0610566237 sf0610565238 6 10566237 3.87E-99 4.10E-31
vg0706905826 sf0706904831 7 6905826 1.31E-63 NA
vg0719132379 sf0719131386 7 19132379 4.41E-63 NA
vg0304920678 sf0304919680 3 4920678 3.61E-61 NA
vg0121675342 sf0121674297 1 21675342 3.59E-60 NA
vg0116643040 sf0116642014 1 16643040 2.79E-57 1.88E-06
vg0127210847 sf0127209803 1 27210847 3.49E-55 4.79E-06
vg0610532672 sf0610531673 6 10532672 NA 5.03E-16
vg0610444069 sf0610443070 6 10444069 NA 2.35E-13
vg0610763769 sf0610762770 6 10763769 NA 5.16E-12
vg0610106910 sf0610105911 6 10106910 NA 1.03E-09
vg0610281727 sf0610280728 6 10281727 NA 8.63E-08
vg0609929059 sf0609928060 6 9929059 NA 2.11E-07
vg0610813890 sf0610812891 6 10813890 NA 2.77E-07
vg0421497689 sf0421325740 4 21497689 NA 3.18E-07
vg0317506741 sf0317505523 3 17506741 NA 3.41E-07
vg0610722873 sf0610721874 6 10722873 NA 3.62E-07
vg0120050864 sf0120049819 1 20050864 NA 3.06E-06
vg1118850288 sf1118384097 11 18850288 NA 3.39E-06
vg0228555700 sf0228549831 2 28555700 NA 3.68E-06
vg0613809145 sf0613808146 6 13809145 NA 3.81E-06
vg1006456919 sf1006472542 10 6456919 NA 4.23E-06
vg0719533358 sf0719532365 7 19533358 NA 4.45E-06
vg0615907055 sf0615906057 6 15907055 NA 4.53E-06
vg0411636513 sf0411627219 4 11636513 NA 4.59E-06
vg0610456976 sf0610455977 6 10456976 NA 4.77E-06
vg0905593689 sf0905592689 9 5593689 NA 7.84E-06