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 mr1057 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
vg0105135246 sf0105134246 1 5135246 1.46E-27 3.37E-25
vg0105145738 sf0105144738 1 5145738 3.40E-27 1.91E-25
vg0105134457 sf0105133457 1 5134457 8.65E-22 4.98E-16
vg1202047032 sf1202046030 12 2047032 3.68E-12 1.68E-07
vg0207368854 sf0207368854 2 7368854 6.29E-12 5.28E-07
vg0703978231 sf0703977232 7 3978231 7.86E-12 NA
vg1022841560 sf1022770033 10 22841560 7.60E-11 8.35E-07
vg1223355966 sf1223322426 12 23355966 1.02E-10 3.33E-07
vg0207379019 sf0207379019 2 7379019 2.86E-10 6.68E-09
vg0723230135 sf0723229142 7 23230135 4.47E-09 1.82E-06
vg1220441290 sf1220412732 12 20441290 1.17E-08 1.44E-06
vg0313235407 sf0313234125 3 13235407 1.20E-08 7.83E-07
vg1221654317 sf1221620864 12 21654317 2.28E-08 1.09E-07
vg1213065934 sf1213063273 12 13065934 9.61E-08 4.41E-07
vg1225476545 sf1225442940 12 25476545 3.42E-07 NA
vg0105166793 sf0105165793 1 5166793 5.02E-07 2.31E-22
vg0335950921 sf0335943790 3 35950921 3.59E-06 3.25E-08
vg0105125030 sf0105124030 1 5125030 NA 4.65E-10
vg0907668817 sf0907667817 9 7668817 NA 4.78E-08
vg0718735755 sf0718734762 7 18735755 NA 9.93E-08
vg0500535025 sf0500535025 5 535025 NA 1.11E-07
vg1020380304 sf1020308784 10 20380304 NA 3.63E-07
vg0420556306 sf0420384350 4 20556306 NA 5.96E-07
vg0127580582 sf0127579538 1 27580582 NA 6.57E-07
vg1221582274 sf1221548821 12 21582274 NA 1.48E-06
vg0522716604 sf0522654046 5 22716604 NA 3.52E-06