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
vg0216822884 sf0216817014 2 16822884 8.06E-52 6.67E-25
vg0217102217 sf0217096347 2 17102217 2.88E-50 2.10E-25
vg0720349785 sf0720348792 7 20349785 5.73E-25 NA
vg0526975009 sf0526912365 5 26975009 3.25E-24 NA
vg0617466298 sf0617465301 6 17466298 4.64E-23 NA
vg0127504883 sf0127503839 1 27504883 5.47E-23 NA
vg1114473442 sf1114009759 11 14473442 3.16E-22 6.31E-07
vg0216576140 sf0216570270 2 16576140 8.27E-22 5.94E-10
vg0218522108 sf0218516239 2 18522108 5.36E-21 2.67E-07
vg0812023942 sf0812022947 8 12023942 1.19E-20 1.74E-08
vg0617033931 sf0617032934 6 17033931 1.37E-17 4.90E-06
vg1213797573 sf1213794911 12 13797573 5.28E-17 7.69E-08
vg0217228197 sf0217222327 2 17228197 NA 2.17E-15
vg0216763667 sf0216757797 2 16763667 NA 4.21E-08
vg0217845805 sf0217839936 2 17845805 NA 4.61E-08
vg0219771380 sf0219765512 2 19771380 NA 1.64E-07
vg1008865540 sf1008794402 10 8865540 NA 6.19E-07
vg0212179963 sf0212179959 2 12179963 NA 1.31E-06
vg1005364262 sf1005380799 10 5364262 NA 1.91E-06
vg0524432058 sf0524369479 5 24432058 NA 2.00E-06
vg0117778414 sf0117777368 1 17778414 NA 3.08E-06
vg0216381476 sf0216375606 2 16381476 NA 4.39E-06
vg1105770829 sf1105766581 11 5770829 NA 4.95E-06