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 mr1374 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
vg0420711795 sf0420539838 4 20711795 5.67E-09 5.67E-09
vg0607692659 sf0607691660 6 7692659 1.01E-07 1.01E-07
vg0122971893 sf0122970849 1 22971893 1.11E-07 1.11E-07
vg0709448532 sf0709447538 7 9448532 2.11E-07 2.11E-07
vg0805826839 sf0805825842 8 5826839 2.56E-07 2.56E-07
vg0516508609 sf0516451091 5 16508609 2.88E-07 2.88E-07
vg0607755458 sf0607754459 6 7755458 3.57E-07 3.57E-07
vg0411665882 sf0411656588 4 11665882 4.46E-07 4.46E-07
vg0717084736 sf0717083743 7 17084736 6.03E-07 6.04E-07
vg0921004343 sf0921003862 9 21004343 6.16E-07 6.17E-07
vg0810920351 sf0810919356 8 10920351 8.73E-07 8.73E-07
vg0819484888 sf0819482175 8 19484888 9.59E-07 9.59E-07
vg0223523255 sf0223517386 2 23523255 1.60E-06 1.60E-06
vg0411938695 sf0411929406 4 11938695 1.66E-06 1.66E-06
vg0826110394 sf0826107680 8 26110394 1.78E-06 1.78E-06
vg0424181194 sf0423996055 4 24181194 2.34E-06 2.34E-06
vg0706405260 sf0706404265 7 6405260 2.35E-06 2.35E-06
vg0715502728 sf0715501735 7 15502728 2.67E-06 2.67E-06
vg0817557507 sf0817554793 8 17557507 2.80E-06 2.81E-06
vg1215307750 sf1215305048 12 15307750 2.87E-06 2.88E-06
vg0801344289 sf0801343291 8 1344289 2.90E-06 2.90E-06