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 mr1750 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
vg0321240772 sf0321239282 3 21240772 3.34E-57 3.89E-27
vg0321187437 sf0321185947 3 21187437 1.29E-53 8.41E-26
vg0320067880 sf0320066391 3 20067880 3.71E-50 9.83E-25
vg0321218610 sf0321217120 3 21218610 4.12E-42 8.03E-16
vg0318543836 sf0318542618 3 18543836 4.47E-41 1.07E-14
vg0320894743 sf0320893253 3 20894743 3.55E-39 2.22E-28
vg0318063509 sf0318062291 3 18063509 1.27E-37 7.73E-21
vg0317756145 sf0317754927 3 17756145 1.15E-34 3.64E-12
vg0321960786 sf0321959293 3 21960786 6.46E-25 1.34E-11
vg0319680247 sf0319678758 3 19680247 1.63E-23 7.28E-11
vg0318003091 sf0318001873 3 18003091 3.35E-23 6.38E-07
vg0321772541 sf0321771051 3 21772541 7.74E-22 8.16E-10
vg0318301991 sf0318300773 3 18301991 3.18E-20 6.75E-10
vg0320662648 sf0320661158 3 20662648 9.43E-20 1.30E-08
vg0318955179 sf0318953939 3 18955179 8.37E-19 2.99E-08
vg0320635449 sf0320633959 3 20635449 6.01E-18 7.74E-09
vg0321402881 sf0321401391 3 21402881 8.98E-18 1.65E-07
vg0322718664 sf0322717153 3 22718664 2.29E-14 4.13E-08
vg0317664128 sf0317662910 3 17664128 1.15E-13 7.56E-09
vg0321143949 sf0321142459 3 21143949 1.85E-13 2.94E-08
vg0322324822 sf0322323311 3 22324822 1.87E-12 8.21E-07
vg0322966434 sf0322964922 3 22966434 NA 3.45E-10
vg1118022065 sf1117555923 11 18022065 NA 3.18E-08
vg1213707083 sf1213704421 12 13707083 NA 4.39E-08
vg0320136332 sf0320134843 3 20136332 NA 5.23E-08
vg0207984549 sf0207984548 2 7984549 NA 7.56E-08
vg0500736167 sf0500736167 5 736167 NA 1.15E-07
vg0522752065 sf0522689507 5 22752065 NA 1.58E-07
vg0524331456 sf0524268875 5 24331456 NA 1.70E-07
vg0327392349 sf0327385402 3 27392349 NA 2.34E-07
vg0207682110 sf0207682110 2 7682110 NA 2.80E-06