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 mr1310 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
vg0106693959 sf0106692959 1 6693959 1.37E-23 8.34E-16
vg0106294787 sf0106293787 1 6294787 5.58E-20 1.42E-14
vg0106064396 sf0106063396 1 6064396 1.23E-13 4.73E-11
vg0518984986 sf0518922470 5 18984986 1.63E-12 5.90E-08
vg0317879120 sf0317877902 3 17879120 2.95E-11 8.28E-06
vg0906477614 sf0906476614 9 6477614 3.33E-11 1.07E-06
vg0404607345 sf0404602948 4 4607345 8.20E-11 9.10E-07
vg1122520841 sf1122054712 11 22520841 8.42E-11 9.53E-07
vg0607348572 sf0607347573 6 7348572 1.37E-10 3.19E-06
vg0601437237 sf0601436238 6 1437237 1.47E-10 3.96E-06
vg0106598597 sf0106597597 1 6598597 2.58E-10 2.96E-06
vg0109768649 sf0109767625 1 9768649 4.05E-09 1.13E-06
vg0119552600 sf0119551555 1 19552600 5.43E-09 1.50E-06
vg1117544237 sf1117078092 11 17544237 4.56E-08 NA
vg0812010568 sf0812009573 8 12010568 1.06E-07 4.93E-07
vg1222743479 sf1222709918 12 22743479 5.77E-07 6.45E-07
vg0906888939 sf0906887939 9 6888939 6.08E-07 1.49E-06
vg1020189984 sf1020118466 10 20189984 6.12E-06 NA
vg0408655352 sf0408650628 4 8655352 6.66E-06 4.73E-06
vg1107375253 sf1107370998 11 7375253 NA 3.46E-06
vg1105377831 sf1105373582 11 5377831 NA 4.33E-06