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 mr1038 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
vg0728442720 sf0728441728 7 28442720 1.30E-27 2.79E-18
vg1222591917 sf1222558356 12 22591917 2.36E-19 1.70E-12
vg0330077379 sf0330070418 3 30077379 2.02E-17 2.59E-09
vg0631155509 sf0631154511 6 31155509 3.30E-17 4.83E-08
vg0202925463 sf0202925461 2 2925463 7.80E-17 9.29E-12
vg0330452376 sf0330445265 3 30452376 3.45E-16 1.45E-09
vg0728693760 sf0728692768 7 28693760 1.05E-15 1.23E-11
vg0728665353 sf0728664361 7 28665353 9.12E-15 9.01E-08
vg0325722534 sf0325720552 3 25722534 2.82E-14 1.11E-08
vg0622846135 sf0622845138 6 22846135 7.45E-13 2.46E-08
vg1223831003 sf1223797456 12 23831003 1.20E-12 1.36E-07
vg1219448842 sf1219420312 12 19448842 1.33E-12 3.45E-09
vg0525542986 sf0525480407 5 25542986 1.63E-12 2.40E-07
vg0526514954 sf0526452318 5 26514954 2.46E-12 2.06E-09
vg0806359100 sf0806358105 8 6359100 1.09E-11 3.80E-08
vg0219929533 sf0219923665 2 19929533 1.41E-11 6.63E-08
vg1217972644 sf1217944080 12 17972644 2.50E-11 2.92E-08
vg0724944841 sf0724943847 7 24944841 5.30E-11 1.03E-07
vg1206967731 sf1206966621 12 6967731 5.85E-11 7.58E-08
vg1017360881 sf1017289654 10 17360881 2.21E-10 2.87E-06
vg1100433021 sf1100432024 11 433021 3.73E-09 6.72E-08
vg0406740172 sf0406735618 4 6740172 3.97E-08 9.36E-08
vg1019343930 sf1019272485 10 19343930 5.94E-06 NA
vg0526356726 sf0526294089 5 26356726 NA 1.48E-08
vg0800237681 sf0800236681 8 237681 NA 2.21E-06