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 mr1715 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
vg0308383505 sf0308382443 3 8383505 5.77E-25 NA
vg0205305769 sf0205305768 2 5305769 8.10E-25 NA
vg0915269390 sf0915268389 9 15269390 2.24E-24 8.01E-07
vg0223067145 sf0223061276 2 23067145 2.32E-24 NA
vg0908613124 sf0908612123 9 8613124 3.62E-24 NA
vg0103416626 sf0103415626 1 3416626 5.43E-20 1.10E-06
vg1125889763 sf1125423682 11 25889763 2.34E-18 NA
vg0219846372 sf0219840504 2 19846372 NA 2.51E-06
vg1107084198 sf1107079943 11 7084198 NA 2.64E-06
vg0234204097 sf0234198228 2 34204097 NA 3.12E-06
vg1022845266 sf1022773739 10 22845266 NA 3.46E-06
vg0123979773 sf0123978729 1 23979773 NA 3.97E-06
vg1126102161 sf1125630575 11 26102161 NA 4.21E-06
vg1218169215 sf1218140651 12 18169215 NA 4.40E-06
vg1217654469 sf1217648424 12 17654469 NA 8.26E-06