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 mr1417 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
vg0819393368 sf0819390655 8 19393368 5.56E-09 5.56E-09
vg0805826839 sf0805825842 8 5826839 4.94E-08 4.94E-08
vg0421030366 sf0420858419 4 21030366 1.18E-07 1.18E-07
vg0817355953 sf0817353239 8 17355953 5.88E-07 5.88E-07
vg0709448532 sf0709447538 7 9448532 7.02E-07 7.01E-07
vg0424924196 sf0424739057 4 24924196 9.24E-07 9.24E-07
vg0122971925 sf0122970881 1 22971925 2.03E-06 2.03E-06
vg1114618741 sf1114155059 11 14618741 2.49E-06 2.49E-06
vg0527942741 sf0527880097 5 27942741 2.79E-06 2.79E-06
vg0704732672 sf0704731673 7 4732672 2.86E-06 2.86E-06
vg0409313344 sf0409308617 4 9313344 2.94E-06 2.95E-06
vg0417276192 sf0417104233 4 17276192 2.98E-06 2.98E-06
vg0905282844 sf0905281844 9 5282844 4.54E-06 4.54E-06
vg0403552516 sf0403548118 4 3552516 4.96E-06 4.96E-06