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 mr1264 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
vg0719141529 sf0719140536 7 19141529 3.27E-14 3.26E-14
vg0719044160 sf0719043167 7 19044160 6.40E-10 6.40E-10
vg0811122650 sf0811121655 8 11122650 2.37E-08 2.37E-08
vg0516162890 sf0516105374 5 16162890 3.71E-08 3.71E-08
vg0707738691 sf0707737696 7 7738691 1.15E-07 1.15E-07
vg0107168392 sf0107167392 1 7168392 1.80E-07 1.80E-07
vg0113100532 sf0113099506 1 13100532 5.13E-07 5.13E-07
vg0419763927 sf0419591962 4 19763927 5.74E-07 5.74E-07
vg1217240367 sf1217234322 12 17240367 7.83E-07 7.83E-07
vg0625385908 sf0625384911 6 25385908 1.67E-06 1.67E-06
vg1023155972 sf1023084444 10 23155972 2.29E-06 2.29E-06
vg0105903122 sf0105902122 1 5903122 3.95E-06 3.94E-06
vg1001317449 sf1001316426 10 1317449 4.78E-06 4.78E-06