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 mr1035 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
vg0405615364 sf0405610805 4 5615364 1.12E-35 3.84E-20
vg0405559634 sf0405555075 4 5559634 3.16E-35 3.04E-20
vg0405560461 sf0405555902 4 5560461 7.21E-35 6.55E-20
vg0410985561 sf0410976262 4 10985561 3.31E-20 1.42E-11
vg0806609517 sf0806608522 8 6609517 2.61E-19 NA
vg1128801855 sf1128278634 11 28801855 5.60E-18 NA
vg0232876236 sf0232870367 2 32876236 2.12E-17 NA
vg0405249563 sf0405245004 4 5249563 9.99E-16 1.77E-10
vg0405636181 sf0405631622 4 5636181 7.13E-15 6.35E-13
vg0405309804 sf0405305245 4 5309804 1.03E-14 1.56E-08
vg0705102263 sf0705101264 7 5102263 1.62E-14 1.30E-06
vg0604084670 sf0604083671 6 4084670 2.71E-14 2.09E-06
vg0136274627 sf0136273584 1 36274627 4.35E-14 1.52E-06
vg0405459967 sf0405455408 4 5459967 1.78E-13 4.39E-06
vg0405223882 sf0405219323 4 5223882 3.35E-13 1.28E-06
vg0405559687 sf0405555128 4 5559687 NA 6.86E-13
vg0408307133 sf0408302407 4 8307133 NA 1.69E-07
vg0410974517 sf0410965218 4 10974517 NA 3.27E-07
vg0407110892 sf0407106162 4 7110892 NA 5.52E-07
vg0405502839 sf0405498280 4 5502839 NA 7.00E-07
vg0412751761 sf0412742471 4 12751761 NA 9.08E-07
vg0405157732 sf0405153174 4 5157732 NA 1.15E-06
vg0405785336 sf0405780775 4 5785336 NA 1.72E-06
vg0405440340 sf0405435781 4 5440340 NA 2.67E-06
vg0118782155 sf0118781110 1 18782155 NA 2.95E-06
vg0702672533 sf0702671534 7 2672533 NA 3.39E-06
vg0815900819 sf0815898105 8 15900819 NA 4.08E-06
vg0804004654 sf0804003657 8 4004654 NA 4.25E-06
vg0118776462 sf0118775417 1 18776462 NA 4.92E-06