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 mr1437 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
vg0719056561 sf0719055568 7 19056561 3.11E-19 9.37E-20
vg0719053396 sf0719052403 7 19053396 1.38E-11 3.92E-14
vg0230093704 sf0230087835 2 30093704 5.48E-07 2.84E-06
vg0901474384 sf0901473384 9 1474384 6.60E-07 1.37E-07
vg0820065663 sf0820062950 8 20065663 1.23E-06 1.19E-06
vg0700416280 sf0700415280 7 416280 3.50E-06 2.46E-07
vg0419763927 sf0419591962 4 19763927 3.69E-06 3.02E-06
vg0413556513 sf0413547227 4 13556513 3.75E-06 9.67E-07
vg0804028565 sf0804027568 8 4028565 NA 4.50E-07
vg0626936733 sf0626935736 6 26936733 NA 9.79E-07
vg0515005729 sf0514948272 5 15005729 NA 1.24E-06
vg1102434606 sf1102430510 11 2434606 NA 1.34E-06
vg0610419166 sf0610418167 6 10419166 NA 2.40E-06
vg0124736255 sf0124735211 1 24736255 NA 2.47E-06
vg0912636580 sf0912635579 9 12636580 NA 2.89E-06
vg0828401472 sf0828398758 8 28401472 NA 3.36E-06
vg0816231145 sf0816228431 8 16231145 NA 4.90E-06