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
vg0719049421 sf0719048428 7 19049421 4.07E-17 8.94E-18
vg0719056561 sf0719055568 7 19056561 4.25E-17 8.00E-20
vg0719006525 sf0719005532 7 19006525 3.92E-12 4.38E-15
vg0230093704 sf0230087835 2 30093704 4.76E-08 1.07E-07
vg0901474384 sf0901473384 9 1474384 1.18E-06 2.99E-07
vg0107198487 sf0107197487 1 7198487 1.24E-06 2.41E-06
vg0419763927 sf0419591962 4 19763927 2.52E-06 4.55E-06
vg0700416280 sf0700415280 7 416280 NA 7.26E-07
vg1102434606 sf1102430510 11 2434606 NA 8.53E-07
vg0413556513 sf0413547227 4 13556513 NA 1.88E-06
vg0408294706 sf0408289980 4 8294706 NA 2.03E-06
vg0124590858 sf0124589814 1 24590858 NA 2.12E-06
vg0820065663 sf0820062950 8 20065663 NA 3.69E-06
vg0422772120 sf0422587003 4 22772120 NA 3.95E-06
vg0610419166 sf0610418167 6 10419166 NA 4.12E-06
vg0626936733 sf0626935736 6 26936733 NA 4.30E-06