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 mr1016 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
vg1215965939 sf1215963235 12 15965939 3.04E-154 1.25E-64
vg1210219854 sf1210217266 12 10219854 2.62E-72 4.00E-06
vg1210217896 sf1210215308 12 10217896 4.00E-72 2.22E-07
vg1224007541 sf1223973994 12 24007541 1.05E-61 NA
vg0217071443 sf0217065573 2 17071443 1.52E-54 NA
vg1219911712 sf1219883182 12 19911712 2.23E-54 NA
vg1212938220 sf1212935559 12 12938220 1.43E-53 5.68E-09
vg1221886540 sf1221853087 12 21886540 2.27E-52 1.69E-06
vg0220486632 sf0220480764 2 20486632 1.14E-45 1.47E-06
vg1215857575 sf1215854871 12 15857575 NA 6.48E-34
vg1215970855 sf1215968151 12 15970855 NA 3.70E-17
vg1215871822 sf1215869118 12 15871822 NA 2.16E-11
vg0610620315 sf0610619316 6 10620315 NA 8.91E-11
vg1216151894 sf1216149190 12 16151894 NA 1.27E-09
vg1216004181 sf1216001477 12 16004181 NA 4.73E-09
vg0521485463 sf0521422904 5 21485463 NA 1.77E-08
vg1215261373 sf1215258671 12 15261373 NA 5.94E-08
vg0401349008 sf0401344558 4 1349008 NA 7.39E-08
vg1216156576 sf1216153872 12 16156576 NA 1.45E-07
vg1209586745 sf1209584154 12 9586745 NA 3.04E-07
vg1216345874 sf1216343170 12 16345874 NA 3.27E-07
vg1212172403 sf1212169740 12 12172403 NA 3.93E-07
vg1215962650 sf1215959946 12 15962650 NA 4.93E-07
vg1217371642 sf1217365597 12 17371642 NA 7.15E-07
vg1018220310 sf1018148869 10 18220310 NA 1.48E-06
vg1215438933 sf1215436231 12 15438933 NA 1.73E-06