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 mr1904 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
vg1102103286 sf1102099144 11 2103286 1.23E-23 2.61E-07
vg1102288326 sf1102284185 11 2288326 9.16E-23 1.31E-07
vg0231850031 sf0231844162 2 31850031 2.23E-19 NA
vg0424107814 sf0423922675 4 24107814 1.70E-18 NA
vg0915918134 sf0915917133 9 15918134 2.64E-18 NA
vg0701510076 sf0701509076 7 1510076 2.73E-18 NA
vg1115243061 sf1114779375 11 15243061 8.26E-16 4.66E-06
vg0507651613 sf0507651554 5 7651613 1.02E-15 NA
vg1212822297 sf1212819636 12 12822297 4.41E-14 NA
vg1012381817 sf1012310632 10 12381817 8.55E-13 NA
vg0322428586 sf0322427075 3 22428586 NA 3.39E-07
vg0206576520 sf0206576520 2 6576520 NA 1.70E-06
vg0421414612 sf0421242665 4 21414612 NA 2.64E-06
vg1224214570 sf1224181023 12 24214570 NA 2.70E-06
vg0507818456 sf0507818397 5 7818456 NA 2.81E-06
vg1122467523 sf1122001394 11 22467523 NA 3.34E-06
vg0427895691 sf0427710553 4 27895691 NA 3.86E-06
vg0906527724 sf0906526724 9 6527724 NA 5.42E-06
vg1119756132 sf1119289820 11 19756132 NA 7.83E-06