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 mr1482 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
vg0908963832 sf0908962831 9 8963832 3.14E-12 NA
vg0507143482 sf0507143424 5 7143482 4.53E-12 NA
vg0105082156 sf0105081156 1 5082156 4.72E-12 NA
vg0431561524 sf0431376420 4 31561524 9.06E-12 NA
vg0105080826 sf0105079826 1 5080826 1.42E-11 NA
vg0527924474 sf0527861831 5 27924474 3.92E-11 NA
vg1017943125 sf1017871897 10 17943125 4.92E-10 4.06E-06
vg0608071379 sf0608070380 6 8071379 1.02E-08 7.19E-08
vg0607961607 sf0607960608 6 7961607 1.30E-08 3.71E-07
vg0820260559 sf0820257846 8 20260559 7.50E-08 8.12E-06
vg0115899007 sf0115897981 1 15899007 1.48E-07 NA
vg0816158006 sf0816155292 8 16158006 3.07E-07 NA
vg0821970212 sf0821967499 8 21970212 NA 4.68E-07
vg0608187813 sf0608186814 6 8187813 NA 6.78E-07
vg0805694237 sf0805693240 8 5694237 NA 1.20E-06
vg0434375534 sf0434190428 4 34375534 NA 2.83E-06
vg0708373669 sf0708372674 7 8373669 NA 4.32E-06
vg1006743994 sf1006759617 10 6743994 NA 4.69E-06
vg0138937464 sf0138936421 1 38937464 NA 9.22E-06