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 mr1257 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
vg0217033543 sf0217027673 2 17033543 8.36E-45 2.11E-30
vg0217023273 sf0217017403 2 17023273 3.16E-44 7.41E-31
vg0812023942 sf0812022947 8 12023942 4.50E-22 4.00E-13
vg0900337327 sf0900336327 9 337327 2.30E-17 8.81E-09
vg0216662827 sf0216656957 2 16662827 2.07E-15 1.24E-09
vg0217737467 sf0217731597 2 17737467 4.89E-15 1.90E-08
vg1005364262 sf1005380799 10 5364262 8.43E-15 2.19E-10
vg0217737425 sf0217731555 2 17737425 1.12E-14 1.47E-08
vg0216104235 sf0216098365 2 16104235 2.21E-13 1.43E-08
vg0217677605 sf0217671735 2 17677605 1.13E-12 1.07E-06
vg1114473442 sf1114009759 11 14473442 2.32E-12 3.57E-07
vg0115588570 sf0115587544 1 15588570 2.42E-11 6.03E-07
vg0216743021 sf0216737151 2 16743021 9.94E-11 1.20E-07
vg0216631549 sf0216625679 2 16631549 1.27E-10 2.89E-07
vg0213916637 sf0213910767 2 13916637 2.30E-10 3.60E-06
vg0216721532 sf0216715662 2 16721532 7.07E-10 2.84E-07
vg1220237604 sf1220209046 12 20237604 1.73E-09 2.63E-06
vg1112889066 sf1112425387 11 12889066 1.33E-08 1.30E-06
vg1105770829 sf1105766581 11 5770829 4.23E-08 2.78E-06
vg0217679975 sf0217674105 2 17679975 4.33E-08 2.37E-07
vg1121625049 sf1121158926 11 21625049 5.49E-06 2.05E-06
vg0217842756 sf0217836887 2 17842756 NA 3.32E-06