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 mr1211 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
vg0610675739 sf0610674740 6 10675739 2.26E-43 3.98E-42
vg0610750291 sf0610749292 6 10750291 1.24E-38 1.66E-26
vg0610539571 sf0610538572 6 10539571 1.39E-38 1.11E-28
vg0610419955 sf0610418956 6 10419955 3.55E-27 3.40E-31
vg0610119624 sf0610118625 6 10119624 3.28E-22 7.93E-18
vg0610119475 sf0610118476 6 10119475 7.13E-22 7.14E-18
vg0610684350 sf0610683351 6 10684350 1.26E-20 3.23E-21
vg0610435285 sf0610434286 6 10435285 1.07E-18 2.87E-20
vg0613050715 sf0613049716 6 13050715 3.36E-15 3.17E-12
vg0610684751 sf0610683752 6 10684751 3.37E-15 7.22E-13
vg0610679932 sf0610678933 6 10679932 1.27E-14 5.89E-15
vg0610847753 sf0610846754 6 10847753 6.10E-14 1.42E-12
vg0616986734 sf0616985737 6 16986734 6.88E-14 1.77E-11
vg0609978936 sf0609977937 6 9978936 1.74E-13 8.12E-10
vg0610382484 sf0610381485 6 10382484 1.36E-12 2.26E-09
vg0611432223 sf0611431224 6 11432223 2.64E-12 2.30E-12
vg0613057898 sf0613056899 6 13057898 3.44E-11 2.36E-08
vg0610287105 sf0610286106 6 10287105 7.99E-11 4.90E-08
vg0615150907 sf0615149908 6 15150907 3.70E-10 8.07E-10
vg0816239139 sf0816236425 8 16239139 5.94E-10 6.82E-09
vg0611389085 sf0611388086 6 11389085 6.92E-10 1.84E-09
vg0610428814 sf0610427815 6 10428814 9.44E-10 6.32E-10
vg0617651311 sf0617650314 6 17651311 8.51E-09 1.44E-08
vg0612193499 sf0612192500 6 12193499 2.27E-06 1.50E-10
vg0610886362 sf0610885363 6 10886362 NA 4.06E-08
vg0612613334 sf0612612335 6 12613334 NA 7.27E-07