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 mr1039 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
vg0506849316 sf0506849258 5 6849316 2.31E-99 2.54E-65
vg0506847525 sf0506847467 5 6847525 3.26E-99 1.20E-65
vg1001247140 sf1001246117 10 1247140 9.70E-34 2.02E-11
vg0511662961 sf0511662891 5 11662961 9.15E-26 2.29E-12
vg0412231824 sf0412222535 4 12231824 2.39E-25 9.99E-10
vg0512332611 sf0512332541 5 12332611 3.01E-25 2.28E-13
vg1213203956 sf1213201294 12 13203956 1.65E-24 1.03E-11
vg1009362967 sf1009291788 10 9362967 4.96E-24 2.19E-10
vg0509650627 sf0509650556 5 9650627 6.32E-23 6.49E-12
vg1002265707 sf1002264684 10 2265707 7.23E-23 1.33E-07
vg0506632837 sf0506632778 5 6632837 1.85E-17 5.72E-10
vg0514678744 sf0514621287 5 14678744 5.98E-14 2.14E-08
vg0620932555 sf0620931558 6 20932555 1.19E-13 4.36E-07
vg0233906724 sf0233900855 2 33906724 4.89E-12 8.72E-08
vg0506874665 sf0506874607 5 6874665 5.21E-12 1.70E-12
vg0505613072 sf0505613010 5 5613072 5.49E-12 2.77E-10
vg0506936871 sf0506936813 5 6936871 3.81E-11 1.34E-09
vg0506835228 sf0506835170 5 6835228 8.84E-11 7.12E-09
vg0514650516 sf0514593059 5 14650516 1.24E-09 2.09E-10
vg0507898758 sf0507898699 5 7898758 1.54E-08 8.76E-11
vg0507254337 sf0507254279 5 7254337 2.37E-07 7.39E-08
vg1211500917 sf1211498253 12 11500917 NA 9.65E-09
vg0601059760 sf0601058761 6 1059760 NA 4.93E-07
vg0618963218 sf0618962221 6 18963218 NA 5.09E-07