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 mr1070 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
vg0416878791 sf0416706833 4 16878791 2.27E-12 3.87E-08
vg1006197978 sf1006213627 10 6197978 6.59E-12 2.92E-09
vg1009151297 sf1009080118 10 9151297 2.39E-11 2.01E-08
vg0407825281 sf0407820549 4 7825281 1.83E-10 2.41E-07
vg0610088164 sf0610087165 6 10088164 3.74E-09 NA
vg0610028238 sf0610027239 6 10028238 1.65E-08 2.82E-06
vg0412478616 sf0412469331 4 12478616 2.24E-07 1.27E-07
vg1009316722 sf1009245543 10 9316722 5.79E-07 1.28E-07
vg1121617620 sf1121151497 11 21617620 1.54E-06 4.61E-07
vg0714251445 sf0714250452 7 14251445 1.78E-06 4.21E-06
vg0813433527 sf0813431080 8 13433527 4.04E-06 3.34E-06
vg0216773530 sf0216767660 2 16773530 5.30E-06 1.10E-06
vg0120844009 sf0120842964 1 20844009 9.60E-06 2.35E-06
vg1216558938 sf1216556231 12 16558938 NA 3.26E-06