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 mr1630 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
vg0228241702 sf0228235833 2 28241702 3.31E-08 3.32E-08
vg0626920669 sf0626919672 6 26920669 6.17E-08 6.18E-08
vg0230805438 sf0230799569 2 30805438 1.13E-07 1.13E-07
vg1001912776 sf1001911753 10 1912776 2.74E-07 2.74E-07
vg1001913172 sf1001912149 10 1913172 4.37E-07 4.38E-07
vg0428063590 sf0427878456 4 28063590 1.60E-06 1.61E-06
vg0729298014 sf0729297022 7 29298014 2.35E-06 2.36E-06
vg0211103624 sf0211103621 2 11103624 2.80E-06 2.81E-06
vg0129595210 sf0129594165 1 29595210 2.91E-06 2.92E-06
vg0121863168 sf0121862123 1 21863168 4.35E-06 4.36E-06
vg1216703203 sf1216697157 12 16703203 4.61E-06 4.61E-06
vg0413281650 sf0413272360 4 13281650 4.87E-06 4.86E-06
vg0626616281 sf0626615284 6 26616281 4.90E-06 4.91E-06