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 mr1354 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
vg0724527960 sf0724526966 7 24527960 1.68E-37 5.45E-52
vg0724495741 sf0724494747 7 24495741 2.12E-37 1.81E-54
vg0724516480 sf0724515486 7 24516480 4.51E-36 3.52E-55
vg0724510628 sf0724509634 7 24510628 4.33E-17 4.55E-18
vg0217836354 sf0217830485 2 17836354 2.02E-15 NA
vg0104343872 sf0104342872 1 4343872 2.77E-15 NA
vg0724360759 sf0724359765 7 24360759 2.05E-14 1.10E-19
vg0724504126 sf0724503132 7 24504126 3.30E-12 6.02E-27
vg0429945960 sf0429760827 4 29945960 1.21E-11 NA
vg0724522889 sf0724521895 7 24522889 1.67E-11 5.28E-11
vg0218382286 sf0218376417 2 18382286 1.88E-10 8.49E-11
vg0400999452 sf0400995004 4 999452 5.76E-10 1.88E-08
vg1117530773 sf1117064628 11 17530773 6.29E-10 8.58E-09
vg0724401667 sf0724400673 7 24401667 9.22E-10 1.40E-27
vg0101055689 sf0101054689 1 1055689 5.89E-09 6.24E-11
vg0724500741 sf0724499747 7 24500741 NA 1.10E-21
vg0724321079 sf0724320085 7 24321079 NA 1.62E-14
vg0724427868 sf0724426874 7 24427868 NA 4.53E-13
vg0724523127 sf0724522133 7 24523127 NA 1.89E-09
vg0101034362 sf0101033362 1 1034362 NA 4.62E-09
vg0319141942 sf0319140702 3 19141942 NA 6.88E-09
vg0311608269 sf0311606987 3 11608269 NA 8.59E-09
vg0331907206 sf0331900083 3 31907206 NA 2.50E-08
vg0800814630 sf0800813632 8 814630 NA 3.45E-08
vg0106794361 sf0106793361 1 6794361 NA 3.49E-08
vg1017092925 sf1017021697 10 17092925 NA 4.86E-08