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 mr1180 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
vg0721356842 sf0721355849 7 21356842 1.14E-25 NA
vg1008185116 sf1008113978 10 8185116 5.28E-24 NA
vg0506134837 sf0506134776 5 6134837 6.61E-24 NA
vg0138427451 sf0138426408 1 38427451 1.21E-23 NA
vg0104261328 sf0104260328 1 4261328 1.61E-23 NA
vg0222739831 sf0222733962 2 22739831 NA 1.18E-14
vg1008839147 sf1008768009 10 8839147 NA 8.97E-08
vg0805546102 sf0805545105 8 5546102 NA 1.10E-06
vg0826805595 sf0826802881 8 26805595 NA 2.90E-06
vg0721894601 sf0721893608 7 21894601 NA 3.82E-06
vg0400660143 sf0400659142 4 660143 NA 5.39E-06
vg0805548044 sf0805547047 8 5548044 NA 6.81E-06