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 mr1085 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
vg0719011406 sf0719010413 7 19011406 1.87E-14 1.13E-11
vg0719316520 sf0719315527 7 19316520 3.70E-13 8.95E-12
vg0719140447 sf0719139454 7 19140447 1.92E-12 1.94E-09
vg0707706006 sf0707705011 7 7706006 1.53E-09 2.90E-06
vg0719242112 sf0719241119 7 19242112 2.67E-09 3.36E-06
vg0707877145 sf0707876150 7 7877145 3.80E-09 1.78E-06
vg0304336341 sf0304335343 3 4336341 9.14E-09 NA
vg1201571140 sf1201570140 12 1571140 1.10E-08 3.26E-06
vg0717197101 sf0717196108 7 17197101 3.63E-08 2.64E-06
vg0806865309 sf0806864314 8 6865309 4.53E-08 2.95E-06
vg1201605678 sf1201604678 12 1605678 1.05E-07 NA
vg0610070340 sf0610069341 6 10070340 1.94E-07 4.65E-06
vg0805916803 sf0805915806 8 5916803 3.11E-06 NA
vg0206102808 sf0206102808 2 6102808 3.92E-06 3.47E-06
vg0908782045 sf0908781044 9 8782045 NA 3.77E-06