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 mr1377 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
vg1122447657 sf1121981528 11 22447657 9.09E-12 1.53E-09
vg1118814088 sf1118347896 11 18814088 4.28E-11 6.27E-08
vg0606853482 sf0606852483 6 6853482 1.43E-10 6.65E-07
vg0217070623 sf0217064753 2 17070623 3.42E-10 2.25E-07
vg1118802157 sf1118335965 11 18802157 3.80E-10 1.45E-07
vg0606936078 sf0606935079 6 6936078 1.51E-09 5.44E-07
vg0216772798 sf0216766928 2 16772798 3.10E-09 1.83E-07
vg0216576140 sf0216570270 2 16576140 5.30E-09 1.67E-06
vg0600397469 sf0600396469 6 397469 7.30E-09 3.16E-06
vg0100946410 sf0100945410 1 946410 8.26E-09 1.17E-06
vg0913012156 sf0913011155 9 13012156 8.36E-09 2.06E-06
vg0915738723 sf0915737722 9 15738723 2.33E-08 8.86E-07
vg0606533311 sf0606532312 6 6533311 7.09E-06 3.77E-06
vg0723191618 sf0723190625 7 23191618 NA 9.58E-07