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 mr1261 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
vg0803532614 sf0803531617 8 3532614 2.77E-07 2.77E-07
vg1221857564 sf1221824111 12 21857564 5.52E-07 5.52E-07
vg1001119761 sf1001118737 10 1119761 6.28E-07 6.28E-07
vg0322429997 sf0322428486 3 22429997 7.06E-07 7.07E-07
vg0416243452 sf0416071485 4 16243452 7.18E-07 7.18E-07
vg1001263764 sf1001262741 10 1263764 9.68E-07 9.69E-07
vg0712075058 sf0712074064 7 12075058 1.03E-06 1.03E-06
vg0512094471 sf0512094401 5 12094471 1.83E-06 1.83E-06
vg0727728522 sf0727727529 7 27728522 1.90E-06 1.91E-06
vg1128795148 sf1128271927 11 28795148 1.96E-06 1.96E-06
vg0508401535 sf0508401463 5 8401535 2.01E-06 2.01E-06
vg1205449240 sf1205448226 12 5449240 2.09E-06 2.09E-06
vg0500723383 sf0500723383 5 723383 2.22E-06 2.22E-06
vg0725674584 sf0725673590 7 25674584 2.68E-06 2.68E-06
vg0324423821 sf0324421900 3 24423821 3.49E-06 3.49E-06
vg1206442588 sf1206441478 12 6442588 4.15E-06 4.15E-06
vg0707257565 sf0707256570 7 7257565 4.31E-06 4.31E-06
vg0419845943 sf0419673979 4 19845943 4.86E-06 4.86E-06
vg0825960083 sf0825957369 8 25960083 4.90E-06 4.91E-06