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 mr1019 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
vg1215967403 sf1215964699 12 15967403 1.88E-12 4.87E-11
vg1215974112 sf1215971408 12 15974112 2.53E-12 4.67E-11
vg1209233335 sf1209230744 12 9233335 1.01E-08 2.09E-07
vg1128937803 sf1128414582 11 28937803 1.66E-08 9.07E-07
vg1209299412 sf1209296821 12 9299412 1.73E-08 2.02E-07
vg1013960383 sf1011852414 10 13960383 3.08E-08 7.07E-07
vg0509878983 sf0509878912 5 9878983 3.75E-08 3.66E-07
vg0335115753 sf0335108623 3 35115753 2.55E-07 1.74E-06
vg0631078445 sf0631077447 6 31078445 2.60E-07 2.98E-06
vg0416544560 sf0416372601 4 16544560 6.97E-07 5.40E-06
vg1207811491 sf1207808897 12 7811491 7.98E-07 3.91E-06
vg0615221080 sf0615220081 6 15221080 1.17E-06 3.90E-06
vg0416574457 sf0416402498 4 16574457 1.63E-06 3.33E-06
vg1011829118 sf1011757933 10 11829118 6.56E-06 2.53E-06