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 mr1238 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
vg1124468452 sf1124002292 11 24468452 1.32E-18 2.58E-15
vg0815631643 sf0815628929 8 15631643 1.74E-13 3.06E-10
vg1124965681 sf1124499521 11 24965681 1.91E-12 1.39E-10
vg0815569034 sf0815566320 8 15569034 4.56E-12 1.55E-09
vg1126943355 sf1126471742 11 26943355 9.90E-12 3.65E-11
vg0811525476 sf0811524481 8 11525476 1.23E-11 1.55E-07
vg1127802372 sf1127330758 11 27802372 3.54E-11 4.51E-12
vg0713133553 sf0713132560 7 13133553 2.14E-10 5.83E-07
vg1206990413 sf1206989303 12 6990413 2.68E-10 2.41E-08
vg0503762591 sf0503762568 5 3762591 5.70E-10 1.27E-09
vg1123203627 sf1122737498 11 23203627 7.44E-10 1.13E-10
vg0802371527 sf0802370530 8 2371527 8.44E-10 8.86E-07
vg1125316910 sf1124850750 11 25316910 1.31E-09 4.11E-09
vg0812016101 sf0812015106 8 12016101 1.89E-09 1.30E-07
vg1015982479 sf1015911251 10 15982479 2.10E-09 4.73E-07
vg1124910912 sf1124444752 11 24910912 2.93E-09 3.72E-07
vg0503840950 sf0503840927 5 3840950 4.77E-09 8.38E-09
vg0521578860 sf0521511524 5 21578860 1.04E-08 2.46E-07
vg1125157024 sf1124690864 11 25157024 1.40E-08 1.26E-07
vg1123834453 sf1123368323 11 23834453 1.96E-08 2.33E-07
vg1124335591 sf1123869435 11 24335591 1.98E-08 1.25E-07
vg1123187392 sf1122721263 11 23187392 1.26E-07 1.28E-07
vg0520798049 sf0520735490 5 20798049 2.10E-07 4.33E-08
vg1125108494 sf1124642334 11 25108494 7.01E-07 1.22E-07