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 mr1748 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
vg0525915477 sf0525852898 5 25915477 2.90E-13 1.67E-08
vg0140366212 sf0140365169 1 40366212 6.44E-12 1.04E-06
vg0306631752 sf0306630752 3 6631752 8.87E-12 2.67E-07
vg0908324423 sf0908323423 9 8324423 1.84E-11 5.82E-07
vg1217884118 sf1217855552 12 17884118 3.66E-11 NA
vg0135598251 sf0135597208 1 35598251 4.15E-11 3.18E-06
vg0405974819 sf0405970260 4 5974819 4.28E-11 2.35E-06
vg1022578749 sf1022507223 10 22578749 5.48E-11 2.20E-06
vg1003750840 sf1003749817 10 3750840 5.77E-11 4.09E-09
vg0212094045 sf0212094041 2 12094045 2.83E-10 2.83E-06
vg0216320398 sf0216314528 2 16320398 4.90E-10 3.60E-06
vg0715701951 sf0715700958 7 15701951 6.45E-10 2.66E-07
vg0608071332 sf0608070333 6 8071332 1.70E-09 4.78E-06
vg1124807083 sf1124340923 11 24807083 3.25E-09 4.77E-06
vg0115989167 sf0115988141 1 15989167 4.45E-09 8.32E-07
vg0408695325 sf0408690601 4 8695325 5.82E-09 4.99E-06
vg0421710470 sf0421538521 4 21710470 8.20E-09 1.32E-06
vg1124652420 sf1124186260 11 24652420 8.33E-09 NA
vg0127278759 sf0127277715 1 27278759 4.33E-08 4.76E-06
vg0332490298 sf0332483171 3 32490298 8.71E-08 NA
vg0608349804 sf0608348805 6 8349804 9.72E-08 NA
vg0102820770 sf0102819770 1 2820770 1.16E-07 NA
vg1203449282 sf1203448282 12 3449282 NA 1.90E-06
vg0208480800 sf0208480799 2 8480800 NA 2.65E-06
vg0225138226 sf0225132357 2 25138226 NA 2.78E-06
vg0208424201 sf0208424200 2 8424201 NA 2.99E-06
vg0231688782 sf0231682913 2 31688782 NA 3.53E-06