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 mr1620 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
vg0719064221 sf0719063228 7 19064221 6.89E-79 3.71E-31
vg0719199004 sf0719198011 7 19199004 9.68E-79 6.06E-33
vg0626823814 sf0626822817 6 26823814 2.46E-54 9.56E-06
vg0626833038 sf0626832041 6 26833038 5.92E-54 7.70E-07
vg0917918788 sf0917917787 9 17918788 1.20E-53 NA
vg0705560234 sf0705559235 7 5560234 2.60E-53 NA
vg0708171948 sf0708170953 7 8171948 4.46E-53 NA
vg0719091461 sf0719090468 7 19091461 NA 2.01E-21
vg0719055344 sf0719054351 7 19055344 NA 1.86E-17
vg0719154140 sf0719153147 7 19154140 NA 3.22E-11
vg0718955684 sf0718954691 7 18955684 NA 1.56E-10
vg0719208973 sf0719207980 7 19208973 NA 3.39E-10
vg0719192174 sf0719191181 7 19192174 NA 9.25E-09
vg0719153233 sf0719152240 7 19153233 NA 2.99E-08
vg0230189175 sf0230183306 2 30189175 NA 3.45E-08
vg0719466615 sf0719465622 7 19466615 NA 4.33E-08
vg0719044743 sf0719043750 7 19044743 NA 5.58E-08
vg1222822194 sf1222788633 12 22822194 NA 2.82E-07
vg0719050776 sf0719049783 7 19050776 NA 3.70E-07
vg0722032999 sf0722032006 7 22032999 NA 6.17E-07
vg0719016083 sf0719015090 7 19016083 NA 7.64E-07
vg0719618102 sf0719617109 7 19618102 NA 8.83E-07
vg0719527870 sf0719526877 7 19527870 NA 1.84E-06
vg0113087370 sf0113086344 1 13087370 NA 2.77E-06
vg0302581223 sf0302580219 3 2581223 NA 2.79E-06
vg0901142260 sf0901141260 9 1142260 NA 2.83E-06
vg0803630208 sf0803629211 8 3630208 NA 3.27E-06