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 mr1613 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
vg0406465683 sf0406461126 4 6465683 1.28E-53 1.83E-35
vg0817327521 sf0817324807 8 17327521 2.34E-15 1.58E-10
vg0807357132 sf0807356137 8 7357132 4.29E-13 2.21E-09
vg0403515281 sf0403510884 4 3515281 8.91E-13 1.97E-06
vg0503312521 sf0503312497 5 3312521 9.78E-12 5.92E-08
vg0823019901 sf0823017188 8 23019901 2.47E-11 1.22E-08
vg1222455166 sf1222421605 12 22455166 4.32E-11 2.12E-07
vg0912175034 sf0912174033 9 12175034 3.29E-10 1.57E-07
vg0234169418 sf0234163549 2 34169418 6.00E-10 1.72E-07
vg0406056639 sf0406052078 4 6056639 1.50E-09 1.20E-08
vg0819433740 sf0819431027 8 19433740 9.58E-08 3.90E-08
vg0503471756 sf0503471733 5 3471756 1.47E-07 NA
vg1105886395 sf1105882147 11 5886395 7.30E-07 3.96E-08
vg1209797289 sf1209794699 12 9797289 1.37E-06 7.93E-07
vg0207917838 sf0207917837 2 7917838 1.72E-06 7.69E-07
vg1216561117 sf1216558410 12 16561117 2.50E-06 4.26E-08
vg0208678243 sf0208678242 2 8678243 2.64E-06 4.42E-07
vg0509256609 sf0509256538 5 9256609 2.82E-06 1.36E-07
vg0134994521 sf0134993478 1 34994521 6.51E-06 6.47E-08
vg1227091155 sf1227057554 12 27091155 6.63E-06 4.64E-08
vg0313206866 sf0313205584 3 13206866 NA 1.25E-07
vg0715830231 sf0715829238 7 15830231 NA 5.34E-07
vg0501033512 sf0501033496 5 1033512 NA 5.48E-07