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 mr1679 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
vg0519586441 sf0519523925 5 19586441 8.29E-28 1.39E-07
vg0519631422 sf0519568906 5 19631422 9.98E-28 4.19E-08
vg0719999375 sf0719998382 7 19999375 2.94E-27 1.82E-07
vg1016930175 sf1016858947 10 16930175 1.63E-25 5.94E-08
vg1016937957 sf1016866729 10 16937957 2.79E-25 2.20E-08
vg1003842426 sf1003841402 10 3842426 5.28E-25 NA
vg0408211190 sf0408206464 4 8211190 1.42E-24 NA
vg0719775322 sf0719774329 7 19775322 1.09E-23 1.20E-07
vg1121898365 sf1121432236 11 21898365 5.23E-23 1.29E-08
vg1121898442 sf1121432313 11 21898442 9.51E-22 1.11E-08
vg0109548538 sf0109547514 1 9548538 3.08E-21 3.38E-07
vg1204623507 sf1204622495 12 4623507 NA 4.89E-09
vg0609333189 sf0609332190 6 9333189 NA 1.91E-08
vg1204426116 sf1204425104 12 4426116 NA 2.16E-08
vg0107054597 sf0107053597 1 7054597 NA 4.07E-08
vg0215951295 sf0215945425 2 15951295 NA 4.82E-08
vg0134374494 sf0134373451 1 34374494 NA 6.35E-08
vg0610070964 sf0610069965 6 10070964 NA 6.35E-08
vg0107026972 sf0107025972 1 7026972 NA 7.61E-08
vg0724426000 sf0724425006 7 24426000 NA 2.46E-07
vg0404806537 sf0404801976 4 4806537 NA 4.22E-07
vg1227422436 sf1227388836 12 27422436 NA 5.58E-07
vg1001981255 sf1001980232 10 1981255 NA 7.34E-07
vg0907397102 sf0907396102 9 7397102 NA 1.07E-06
vg0432660385 sf0432475274 4 32660385 NA 1.17E-06
vg1121947567 sf1121481438 11 21947567 NA 1.24E-06
vg0134393590 sf0134392547 1 34393590 NA 1.40E-06
vg0129059051 sf0129058006 1 29059051 NA 1.62E-06
vg0605964534 sf0605963535 6 5964534 NA 1.79E-06
vg0207316810 sf0207316810 2 7316810 NA 1.94E-06