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 mr1841 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
vg1124468452 sf1124002292 11 24468452 1.42E-22 1.41E-17
vg1125147847 sf1124681687 11 25147847 2.24E-19 8.54E-19
vg0815631643 sf0815628929 8 15631643 5.87E-14 1.46E-10
vg1124331341 sf1123865211 11 24331341 7.84E-14 1.41E-13
vg1124341241 sf1123875085 11 24341241 1.58E-13 1.62E-11
vg1124965681 sf1124499521 11 24965681 4.10E-13 2.20E-13
vg0811525476 sf0811524481 8 11525476 1.87E-12 2.35E-06
vg1124348003 sf1123881847 11 24348003 2.70E-12 1.80E-09
vg0113026938 sf0113025912 1 13026938 2.11E-11 2.71E-07
vg1206990413 sf1206989303 12 6990413 3.48E-11 9.61E-09
vg0812016101 sf0812015106 8 12016101 5.75E-11 1.91E-07
vg1127802372 sf1127330758 11 27802372 8.00E-11 3.46E-12
vg1123203627 sf1122737498 11 23203627 8.49E-11 2.60E-10
vg0503762591 sf0503762568 5 3762591 1.80E-10 5.11E-09
vg1015983381 sf1015912153 10 15983381 2.18E-10 4.59E-08
vg1124340538 sf1123874382 11 24340538 7.24E-10 5.25E-08
vg0521578860 sf0521511524 5 21578860 7.59E-10 1.86E-08
vg1125116625 sf1124650465 11 25116625 2.60E-08 3.79E-08
vg0102329091 sf0102328091 1 2329091 7.69E-08 1.22E-07
vg0520747897 sf0520685338 5 20747897 1.80E-07 6.52E-08
vg0224288814 sf0224282945 2 24288814 3.93E-07 1.98E-07
vg1124950335 sf1124484175 11 24950335 1.27E-06 1.80E-07
vg1125108494 sf1124642334 11 25108494 NA 5.37E-07
vg0213822496 sf0213816626 2 13822496 NA 4.60E-06