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 mr1695 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
vg0610001965 sf0610000966 6 10001965 2.09E-24 3.11E-21
vg0610073155 sf0610072156 6 10073155 8.93E-18 1.28E-10
vg0609889578 sf0609888579 6 9889578 1.46E-17 1.21E-13
vg0609999077 sf0609998078 6 9999077 2.82E-15 1.54E-13
vg0611642002 sf0611641003 6 11642002 5.26E-15 1.34E-10
vg0610761751 sf0610760752 6 10761751 1.96E-13 7.84E-14
vg0610597853 sf0610596854 6 10597853 7.30E-13 2.90E-09
vg0610398034 sf0610397035 6 10398034 5.85E-12 2.39E-09
vg0610554368 sf0610553369 6 10554368 1.22E-11 8.87E-10
vg0620971322 sf0620970325 6 20971322 1.41E-11 7.23E-08
vg0618988041 sf0618987044 6 18988041 4.57E-11 4.25E-08
vg0610453680 sf0610452681 6 10453680 1.14E-10 1.47E-07
vg0621488776 sf0621487779 6 21488776 5.60E-09 4.30E-08
vg1116841704 sf1116376583 11 16841704 1.14E-06 8.48E-07
vg0606520607 sf0606519608 6 6520607 1.16E-06 NA
vg0420368452 sf0420196496 4 20368452 2.90E-06 2.61E-06
vg0610132375 sf0610131376 6 10132375 3.23E-06 3.97E-08
vg1104325526 sf1104321428 11 4325526 5.27E-06 9.82E-07
vg1116841607 sf1116376486 11 16841607 6.06E-06 1.21E-06
vg0609896125 sf0609895126 6 9896125 NA 4.23E-11
vg0601362892 sf0601361893 6 1362892 NA 5.51E-07
vg0817393582 sf0817390868 8 17393582 NA 2.41E-06