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 mr1693 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
vg1204622168 sf1204621156 12 4622168 3.33E-19 7.80E-13
vg1204623065 sf1204622053 12 4623065 1.58E-16 2.68E-11
vg0720805926 sf0720804933 7 20805926 5.90E-16 3.53E-12
vg0105931184 sf0105930184 1 5931184 1.93E-14 8.54E-09
vg1223869700 sf1223836153 12 23869700 1.04E-13 1.98E-08
vg0316718408 sf0316717054 3 16718408 1.45E-13 1.86E-08
vg0630108409 sf0630107411 6 30108409 4.03E-13 1.10E-06
vg1122414487 sf1121948358 11 22414487 4.78E-13 2.21E-08
vg0625443240 sf0625442243 6 25443240 5.91E-13 7.51E-10
vg0233059202 sf0233053333 2 33059202 9.07E-13 3.58E-09
vg0222717674 sf0222711805 2 22717674 1.39E-12 1.13E-08
vg1217046463 sf1217040417 12 17046463 1.91E-12 3.57E-08
vg0334873774 sf0334866644 3 34873774 3.37E-12 8.40E-07
vg1123842547 sf1123376417 11 23842547 8.63E-12 1.59E-07
vg1224009039 sf1223975492 12 24009039 8.08E-11 8.86E-07
vg0300339486 sf0300338484 3 339486 3.61E-10 1.34E-06
vg0225199712 sf0225193843 2 25199712 5.80E-09 7.65E-07
vg0114798761 sf0114797735 1 14798761 6.54E-08 6.75E-07
vg0907093222 sf0907092222 9 7093222 4.03E-07 5.97E-07
vg0107540423 sf0107539423 1 7540423 6.39E-07 NA
vg0904840774 sf0904839774 9 4840774 1.04E-06 5.43E-07
vg1016762504 sf1016691277 10 16762504 NA 1.75E-07
vg0414235648 sf0414226361 4 14235648 NA 1.31E-06
vg0828406935 sf0828404221 8 28406935 NA 8.25E-06