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 mr1484 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 1.54E-19 1.89E-16
vg0815631643 sf0815628929 8 15631643 3.43E-13 1.31E-09
vg1127797000 sf1127325386 11 27797000 1.95E-12 4.92E-12
vg0815569034 sf0815566320 8 15569034 2.29E-12 1.94E-09
vg1127802372 sf1127330758 11 27802372 4.45E-12 1.16E-12
vg1127793664 sf1127322050 11 27793664 4.39E-11 2.03E-10
vg0811525476 sf0811524481 8 11525476 4.89E-11 3.67E-07
vg1206990413 sf1206989303 12 6990413 9.22E-11 2.80E-09
vg1125316910 sf1124850750 11 25316910 7.58E-10 1.57E-09
vg1123203627 sf1122737498 11 23203627 9.77E-10 1.61E-10
vg1124348003 sf1123881847 11 24348003 1.11E-09 5.43E-08
vg1015982479 sf1015911251 10 15982479 1.44E-09 2.78E-07
vg0811932204 sf0811931209 8 11932204 1.94E-09 1.49E-08
vg1124965681 sf1124499521 11 24965681 2.60E-09 3.64E-08
vg1123834453 sf1123368323 11 23834453 8.74E-09 8.42E-08
vg0502683697 sf0502683673 5 2683697 1.18E-08 2.84E-08
vg0521578860 sf0521511524 5 21578860 1.18E-08 2.54E-07
vg0715539794 sf0715538801 7 15539794 1.57E-08 1.45E-07
vg1215960919 sf1215958215 12 15960919 2.71E-08 4.77E-08
vg1123187392 sf1122721263 11 23187392 3.10E-08 1.90E-08
vg1125157024 sf1124690864 11 25157024 3.12E-08 4.63E-07
vg1216192863 sf1216190159 12 16192863 1.11E-07 4.05E-07
vg1124933495 sf1124467335 11 24933495 5.25E-07 1.14E-07
vg0520798049 sf0520735490 5 20798049 1.79E-06 2.75E-07