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 mr1719 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
vg1213066215 sf1213063554 12 13066215 4.73E-10 4.17E-08
vg0114895999 sf0114894973 1 14895999 7.38E-10 4.18E-09
vg1000628134 sf1000627110 10 628134 8.16E-09 3.35E-06
vg1213685109 sf1213682447 12 13685109 1.81E-07 4.56E-07
vg0118023767 sf0118022721 1 18023767 2.84E-07 3.15E-06
vg1127472745 sf1127001132 11 27472745 1.96E-06 1.51E-08
vg0713863434 sf0713862441 7 13863434 3.07E-06 3.90E-06
vg0410781389 sf0410772091 4 10781389 5.06E-06 8.75E-07
vg1209813313 sf1209810723 12 9813313 NA 5.41E-08
vg1114450021 sf1113986338 11 14450021 NA 2.78E-07
vg0435422369 sf0435237248 4 35422369 NA 5.61E-07
vg1213063657 sf1213060996 12 13063657 NA 8.37E-07
vg1213778690 sf1213776028 12 13778690 NA 2.63E-06
vg1104766707 sf1104762609 11 4766707 NA 3.04E-06
vg0401127787 sf0401123337 4 1127787 NA 3.10E-06
vg0223405623 sf0223399754 2 23405623 NA 3.67E-06