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 mr1599 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
vg0216679868 sf0216673998 2 16679868 1.76E-32 9.09E-24
vg0216727586 sf0216721716 2 16727586 1.67E-31 4.17E-24
vg0216721532 sf0216715662 2 16721532 5.24E-16 1.28E-13
vg0217737425 sf0217731555 2 17737425 5.08E-15 5.07E-10
vg0213525745 sf0213525741 2 13525745 6.23E-15 1.57E-09
vg0812023942 sf0812022947 8 12023942 7.37E-14 4.60E-09
vg0900336799 sf0900335799 9 336799 2.62E-13 2.51E-08
vg0216624375 sf0216618505 2 16624375 1.05E-12 1.09E-07
vg0216662827 sf0216656957 2 16662827 2.38E-12 6.87E-08
vg1209798487 sf1209795897 12 9798487 3.35E-12 1.18E-08
vg0217677243 sf0217671373 2 17677243 4.73E-12 5.63E-08
vg1005364262 sf1005380799 10 5364262 3.85E-11 3.77E-09
vg0216773376 sf0216767506 2 16773376 4.45E-11 1.68E-09
vg0805785661 sf0805784664 8 5785661 6.17E-11 3.21E-07
vg0217412542 sf0217406672 2 17412542 7.55E-10 5.28E-07
vg0220342684 sf0220336816 2 20342684 1.27E-09 1.60E-07
vg0218552586 sf0218546717 2 18552586 1.82E-09 4.93E-07
vg0216646134 sf0216640264 2 16646134 2.77E-09 5.54E-09
vg0216743021 sf0216737151 2 16743021 4.23E-08 3.91E-07
vg1112889066 sf1112425387 11 12889066 1.68E-07 5.23E-07
vg0525763680 sf0525701101 5 25763680 1.13E-06 3.41E-07
vg0519673741 sf0519611225 5 19673741 NA 3.64E-06
vg0116423619 sf0116422593 1 16423619 NA 8.50E-06