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 mr1617 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
vg0604357002 sf0604356003 6 4357002 2.22E-58 4.72E-30
vg0207150816 sf0207150816 2 7150816 5.01E-35 1.64E-09
vg0313641931 sf0313640648 3 13641931 7.58E-34 3.25E-09
vg0913424446 sf0913423445 9 13424446 4.20E-33 2.77E-08
vg1000865461 sf1000864437 10 865461 9.41E-33 2.95E-08
vg0910028393 sf0910027392 9 10028393 1.07E-31 3.34E-08
vg0913482728 sf0913481727 9 13482728 1.16E-31 6.48E-09
vg1000904013 sf1000902989 10 904013 7.99E-31 3.66E-09
vg0314756039 sf0314754726 3 14756039 1.17E-30 1.41E-09
vg0141843218 sf0141842175 1 41843218 1.47E-30 6.50E-08
vg0508706913 sf0508706841 5 8706913 2.85E-30 3.59E-07
vg0135598251 sf0135597208 1 35598251 1.49E-29 2.91E-08
vg0822420377 sf0822417664 8 22420377 2.17E-28 2.65E-07
vg0216502492 sf0216496622 2 16502492 2.95E-28 7.50E-08
vg1123278155 sf1122812025 11 23278155 7.66E-28 3.10E-08
vg0702730576 sf0702729577 7 2730576 2.04E-27 5.03E-07
vg1223038204 sf1223004664 12 23038204 1.14E-26 7.82E-08
vg0518884062 sf0518821546 5 18884062 1.08E-25 3.34E-07
vg0604237628 sf0604236629 6 4237628 NA 2.24E-12
vg0604336775 sf0604335776 6 4336775 NA 4.27E-12
vg0604439758 sf0604438759 6 4439758 NA 2.14E-10
vg0604317901 sf0604316902 6 4317901 NA 5.29E-10
vg0701270194 sf0701269194 7 1270194 NA 6.26E-08
vg0313141983 sf0313140701 3 13141983 NA 1.06E-07
vg1114274296 sf1113810617 11 14274296 NA 1.54E-07
vg0520503574 sf0520441045 5 20503574 NA 1.86E-07
vg1126454250 sf1125982663 11 26454250 NA 2.24E-07
vg0308093586 sf0308092524 3 8093586 NA 3.23E-07
vg0601465470 sf0601464471 6 1465470 NA 4.61E-07