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 mr1736 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
vg1002234112 sf1002233089 10 2234112 5.69E-09 5.72E-09
vg1002385115 sf1002384092 10 2385115 1.56E-08 1.55E-08
vg0431719457 sf0431534350 4 31719457 1.29E-07 1.29E-07
vg0432449081 sf0432263973 4 32449081 1.44E-07 1.44E-07
vg0709292761 sf0709291767 7 9292761 1.97E-07 1.98E-07
vg1000706431 sf1000705407 10 706431 4.85E-07 4.86E-07
vg1121919833 sf1121453704 11 21919833 6.08E-07 6.08E-07
vg0432692714 sf0432507603 4 32692714 7.97E-07 7.99E-07
vg0414551751 sf0414542465 4 14551751 8.96E-07 9.00E-07
vg1002908137 sf1002907114 10 2908137 1.07E-06 1.07E-06
vg1217073354 sf1217067309 12 17073354 1.52E-06 1.53E-06
vg1002718424 sf1002717401 10 2718424 2.07E-06 2.08E-06
vg0802054564 sf0802053567 8 2054564 2.48E-06 2.49E-06
vg1127566128 sf1127094515 11 27566128 3.12E-06 3.11E-06
vg0414546553 sf0414537267 4 14546553 4.01E-06 4.02E-06
vg0909926383 sf0909925382 9 9926383 4.20E-06 4.21E-06
vg1205788235 sf1205787217 12 5788235 4.31E-06 4.33E-06
vg1017015778 sf1016944550 10 17015778 4.45E-06 4.47E-06