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 mr1792 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
vg1215976850 sf1215974146 12 15976850 8.17E-15 1.33E-07
vg1210519897 sf1210517310 12 10519897 1.42E-13 8.10E-08
vg1215615147 sf1215612444 12 15615147 2.41E-13 3.28E-09
vg1218284485 sf1218255921 12 18284485 2.74E-13 4.50E-08
vg1211970311 sf1211967646 12 11970311 7.56E-11 2.02E-07
vg1213247003 sf1213244341 12 13247003 1.18E-10 NA
vg1223902347 sf1223868800 12 23902347 2.50E-10 NA
vg0805622896 sf0805621899 8 5622896 9.02E-10 2.35E-06
vg1210023864 sf1210021275 12 10023864 9.21E-10 1.08E-08
vg0606077149 sf0606076150 6 6077149 3.70E-07 4.14E-06
vg1200181597 sf1200180597 12 181597 NA 1.49E-06
vg0621365920 sf0621364923 6 21365920 NA 4.25E-06
vg0500284824 sf0500284824 5 284824 NA 4.73E-06