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 mr1137 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
vg0604305910 sf0604304911 6 4305910 1.91E-81 1.37E-40
vg0726347713 sf0726346719 7 26347713 3.51E-45 1.41E-08
vg1224270680 sf1224237133 12 24270680 6.08E-45 1.15E-09
vg0311662859 sf0311661577 3 11662859 2.18E-44 3.96E-11
vg0420495425 sf0420323469 4 20495425 2.18E-43 5.62E-09
vg0508706913 sf0508706841 5 8706913 4.61E-43 3.79E-12
vg0207150816 sf0207150816 2 7150816 1.23E-42 1.09E-09
vg0913424446 sf0913423445 9 13424446 2.29E-42 9.28E-09
vg0327376146 sf0327369199 3 27376146 1.61E-41 2.35E-08
vg0314622952 sf0314621639 3 14622952 2.36E-40 2.57E-08
vg0729244062 sf0729243070 7 29244062 2.54E-40 1.81E-08
vg0609221063 sf0609220064 6 9221063 6.37E-40 6.61E-11
vg0702730576 sf0702729577 7 2730576 2.66E-39 1.99E-09
vg0725422656 sf0725421662 7 25422656 1.29E-38 1.08E-08
vg1000904013 sf1000902989 10 904013 2.21E-35 5.92E-09
vg1117445573 sf1116979428 11 17445573 6.97E-35 1.41E-10
vg0909378209 sf0909377208 9 9378209 1.08E-34 1.16E-08
vg0513751611 sf0513694155 5 13751611 1.11E-32 1.97E-09
vg0617467114 sf0617466117 6 17467114 9.99E-32 NA
vg0604425979 sf0604424980 6 4425979 NA 3.60E-17
vg0604429481 sf0604428482 6 4429481 NA 1.29E-16
vg0604439758 sf0604438759 6 4439758 NA 5.92E-16
vg0604303918 sf0604302919 6 4303918 NA 8.13E-14
vg0604288046 sf0604287047 6 4288046 NA 1.69E-12
vg0701257849 sf0701256849 7 1257849 NA 1.65E-10
vg0601502296 sf0601501297 6 1502296 NA 1.44E-09
vg1119834892 sf1119369433 11 19834892 NA 3.73E-09
vg1011204876 sf1011133696 10 11204876 NA 8.88E-09
vg1013288420 sf1013217189 10 13288420 NA 3.03E-07