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 mr1133 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
vg1125464486 sf1124998325 11 25464486 1.21E-32 1.24E-17
vg0713261979 sf0713260986 7 13261979 4.92E-23 1.33E-09
vg0612546146 sf0612545147 6 12546146 7.99E-21 2.47E-10
vg1127651021 sf1127179408 11 27651021 1.72E-13 2.49E-06
vg1125867362 sf1125401281 11 25867362 5.83E-12 NA
vg1127764793 sf1127293179 11 27764793 1.11E-11 4.79E-07
vg1125797847 sf1125331768 11 25797847 2.39E-11 1.40E-06
vg1126328140 sf1125856553 11 26328140 1.10E-09 2.62E-06
vg1126325661 sf1125854074 11 26325661 1.91E-09 3.50E-07
vg1125603546 sf1125137385 11 25603546 8.58E-09 1.69E-06
vg0612545907 sf0612544908 6 12545907 3.66E-08 3.23E-06
vg1216530566 sf1216527859 12 16530566 1.42E-07 1.73E-06
vg0906460381 sf0906459381 9 6460381 1.77E-06 2.55E-06
vg0517733302 sf0517672943 5 17733302 2.11E-06 NA
vg1204022539 sf1204021527 12 4022539 4.49E-06 4.24E-06
vg0814639996 sf0814637282 8 14639996 NA 2.30E-06
vg1213198370 sf1213195708 12 13198370 NA 4.92E-06