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 mr1437 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
vg0719011406 sf0719010413 7 19011406 2.09E-61 8.38E-18
vg0719049906 sf0719048913 7 19049906 1.17E-56 3.07E-29
vg0305273083 sf0305272083 3 5273083 4.74E-47 NA
vg0707654721 sf0707653726 7 7654721 5.60E-47 NA
vg0917810635 sf0917809634 9 17810635 6.42E-46 NA
vg0704138796 sf0704137797 7 4138796 1.67E-45 NA
vg0315357234 sf0315355881 3 15357234 3.06E-40 1.41E-07
vg0719091461 sf0719090468 7 19091461 NA 4.06E-24
vg0719055344 sf0719054351 7 19055344 NA 5.37E-18
vg0718955684 sf0718954691 7 18955684 NA 3.23E-11
vg0719132485 sf0719131492 7 19132485 NA 3.74E-11
vg0718999754 sf0718998761 7 18999754 NA 1.94E-08
vg0719466615 sf0719465622 7 19466615 NA 3.85E-08
vg0901040131 sf0901039131 9 1040131 NA 3.00E-07
vg0801031318 sf0801030320 8 1031318 NA 3.88E-07
vg0329561125 sf0329554165 3 29561125 NA 5.02E-07
vg0718879158 sf0718878165 7 18879158 NA 7.39E-07
vg1214799785 sf1214797126 12 14799785 NA 1.23E-06
vg1100571681 sf1100570684 11 571681 NA 1.60E-06
vg0418079489 sf0417907530 4 18079489 NA 1.65E-06
vg0428494128 sf0428308982 4 28494128 NA 2.18E-06
vg0720529894 sf0720528901 7 20529894 NA 2.51E-06
vg0424638529 sf0424453391 4 24638529 NA 3.24E-06
vg1217507757 sf1217501712 12 17507757 NA 3.33E-06
vg0719339718 sf0719338725 7 19339718 NA 3.60E-06
vg0631160329 sf0631159331 6 31160329 NA 4.58E-06