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 mr1975 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
vg1105907484 sf1105903236 11 5907484 1.23E-09 3.89E-06
vg1105448751 sf1105444502 11 5448751 6.71E-09 NA
vg1217039777 sf1217033731 12 17039777 7.49E-09 NA
vg0133176308 sf0133175264 1 33176308 9.33E-09 NA
vg0200743118 sf0200743118 2 743118 1.44E-08 NA
vg0200748455 sf0200748455 2 748455 3.95E-08 5.53E-06
vg1000659191 sf1000658167 10 659191 8.05E-08 NA
vg1105431576 sf1105427327 11 5431576 1.48E-07 NA
vg0141963550 sf0141962507 1 41963550 2.58E-07 4.38E-06
vg0310177475 sf0310176391 3 10177475 1.12E-06 6.78E-07
vg0420830218 sf0420658261 4 20830218 NA 1.81E-06