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 mr1609 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
vg1124965463 sf1124499303 11 24965463 8.64E-34 4.46E-12
vg1124970199 sf1124504039 11 24970199 1.75E-33 5.61E-12
vg1125024893 sf1124558733 11 25024893 4.15E-28 2.88E-09
vg1124875808 sf1124409648 11 24875808 4.90E-28 2.30E-14
vg0333901227 sf0333894097 3 33901227 1.01E-27 NA
vg0628364898 sf0628363900 6 28364898 1.59E-27 NA
vg0304250950 sf0304249952 3 4250950 3.23E-27 NA
vg1205254532 sf1205253518 12 5254532 6.85E-27 NA
vg1125118463 sf1124652303 11 25118463 4.40E-25 5.58E-19
vg0308557129 sf0308556067 3 8557129 5.26E-23 NA
vg1124989458 sf1124523298 11 24989458 NA 9.62E-17
vg1124986792 sf1124520632 11 24986792 NA 1.75E-12
vg1125100181 sf1124634021 11 25100181 NA 3.24E-12
vg1125080303 sf1124614143 11 25080303 NA 3.60E-09
vg1124965681 sf1124499521 11 24965681 NA 1.09E-08
vg1125233443 sf1124767283 11 25233443 NA 1.63E-08
vg1124840128 sf1124373968 11 24840128 NA 1.69E-08
vg1125113390 sf1124647230 11 25113390 NA 2.86E-08
vg1124997485 sf1124531325 11 24997485 NA 3.28E-08
vg1125089276 sf1124623116 11 25089276 NA 5.67E-08
vg1125768179 sf1125302018 11 25768179 NA 2.00E-07
vg1124320687 sf1123854557 11 24320687 NA 3.06E-07
vg1124410475 sf1123944319 11 24410475 NA 4.69E-07
vg1124714625 sf1124248465 11 24714625 NA 5.64E-07
vg1125583842 sf1125117681 11 25583842 NA 1.21E-06
vg1214637266 sf1214634606 12 14637266 NA 1.68E-06
vg0606540226 sf0606539227 6 6540226 NA 2.24E-06
vg1125602304 sf1125136143 11 25602304 NA 2.54E-06
vg1124897837 sf1124431677 11 24897837 NA 2.61E-06
vg1122495069 sf1122028940 11 22495069 NA 3.96E-06
vg1124469615 sf1124003455 11 24469615 NA 4.24E-06