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 mr1088 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
vg0719007567 sf0719006574 7 19007567 3.03E-35 1.24E-25
vg0719119966 sf0719118973 7 19119966 2.32E-14 5.61E-08
vg1201625779 sf1201624779 12 1625779 5.02E-14 4.81E-08
vg0719140489 sf0719139496 7 19140489 8.13E-14 2.50E-09
vg0718862824 sf0718861831 7 18862824 4.93E-13 8.46E-10
vg0719338225 sf0719337232 7 19338225 1.79E-12 1.95E-08
vg0717227488 sf0717226495 7 17227488 4.34E-12 2.50E-08
vg0235249589 sf0235243720 2 35249589 1.26E-11 1.23E-08
vg0719453364 sf0719452371 7 19453364 1.88E-11 1.66E-10
vg0719601182 sf0719600189 7 19601182 2.24E-11 6.32E-07
vg0719459563 sf0719458570 7 19459563 2.44E-11 4.15E-08
vg0431597089 sf0431411984 4 31597089 2.55E-10 2.54E-07
vg0719143007 sf0719142014 7 19143007 5.55E-10 9.29E-09
vg1214119394 sf1214116734 12 14119394 7.27E-09 1.23E-06
vg0719192085 sf0719191092 7 19192085 2.21E-08 1.45E-07
vg0718888579 sf0718887586 7 18888579 3.78E-08 2.18E-06
vg0216351953 sf0216346083 2 16351953 4.37E-08 1.84E-06
vg0226057933 sf0226052064 2 26057933 7.03E-08 1.86E-06
vg0106717996 sf0106716996 1 6717996 1.49E-07 NA
vg0228211407 sf0228205538 2 28211407 4.34E-07 2.40E-07
vg0414170889 sf0414161605 4 14170889 4.75E-07 2.13E-06
vg0718985745 sf0718984752 7 18985745 NA 6.81E-08