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 mr1253 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
vg0216752678 sf0216746808 2 16752678 1.83E-26 5.98E-20
vg0217047369 sf0217041499 2 17047369 1.38E-25 5.95E-20
vg0216370112 sf0216364242 2 16370112 5.14E-14 3.07E-08
vg0213525745 sf0213525741 2 13525745 1.42E-13 2.66E-08
vg0216381006 sf0216375136 2 16381006 3.91E-12 5.31E-09
vg0812023942 sf0812022947 8 12023942 2.67E-11 4.53E-06
vg0217861925 sf0217856056 2 17861925 3.29E-09 4.58E-07
vg0218101998 sf0218096129 2 18101998 3.57E-09 3.92E-06
vg0525763678 sf0525701099 5 25763678 3.22E-07 1.47E-06
vg0217291492 sf0217285622 2 17291492 5.69E-07 7.62E-07
vg0524882575 sf0524819990 5 24882575 4.49E-06 NA
vg0216876069 sf0216870199 2 16876069 NA 9.32E-07
vg0615635376 sf0615634378 6 15635376 NA 1.03E-06