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 mr1794 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
vg1009110069 sf1009038930 10 9110069 7.63E-28 3.64E-10
vg1006364647 sf1006380270 10 6364647 4.93E-24 2.00E-08
vg1008447547 sf1008376409 10 8447547 2.42E-19 2.35E-10
vg1216843085 sf1216837039 12 16843085 1.00E-18 2.83E-08
vg0407823910 sf0407819178 4 7823910 1.44E-18 2.25E-06
vg1009148414 sf1009077235 10 9148414 1.37E-17 5.33E-08
vg0407825796 sf0407821064 4 7825796 3.88E-17 4.90E-07
vg1007376266 sf1007391889 10 7376266 4.46E-17 3.70E-12
vg0528707471 sf0528644826 5 28707471 9.15E-16 2.29E-07
vg1216843191 sf1216837145 12 16843191 1.45E-15 5.58E-10
vg1007581845 sf1007597457 10 7581845 1.90E-15 2.78E-11
vg0412853605 sf0412844314 4 12853605 5.99E-14 1.43E-06
vg0910781014 sf0910780013 9 10781014 7.54E-10 1.92E-06
vg0502210759 sf0502210734 5 2210759 1.41E-09 4.43E-07
vg0718482716 sf0718481723 7 18482716 2.54E-09 4.59E-06
vg1006505490 sf1006521113 10 6505490 NA 5.45E-08
vg1006540721 sf1006556344 10 6540721 NA 8.60E-07
vg0705168219 sf0705167220 7 5168219 NA 3.30E-06
vg1008555904 sf1008484766 10 8555904 NA 4.43E-06
vg1006277470 sf1006293093 10 6277470 NA 4.46E-06
vg1203199364 sf1203198367 12 3199364 NA 4.62E-06
vg0910796349 sf0910795348 9 10796349 NA 7.56E-06