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 mr1680 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
vg0221812870 sf0221807001 2 21812870 2.94E-19 5.83E-12
vg1117900742 sf1117434600 11 17900742 1.27E-18 2.25E-06
vg1117949081 sf1117482939 11 17949081 1.41E-17 6.57E-09
vg0424388725 sf0424203586 4 24388725 6.56E-17 NA
vg0430594199 sf0430409074 4 30594199 7.62E-17 7.51E-10
vg0304042116 sf0304041112 3 4042116 8.04E-17 6.81E-06
vg0430613783 sf0430428658 4 30613783 4.71E-16 3.02E-10
vg0129132964 sf0129131919 1 29132964 1.59E-15 2.75E-06
vg1023072667 sf1023001140 10 23072667 7.51E-14 2.29E-06
vg0300939247 sf0300938245 3 939247 8.78E-14 2.16E-07
vg1206186379 sf1206185270 12 6186379 1.17E-13 1.66E-06
vg0430479763 sf0430294641 4 30479763 1.27E-12 1.61E-06
vg1105649773 sf1105645525 11 5649773 2.14E-11 2.14E-07
vg1105644697 sf1105640449 11 5644697 2.24E-11 1.57E-07
vg1014028348 sf1013957114 10 14028348 3.04E-10 2.83E-07
vg1001247771 sf1001246748 10 1247771 NA 8.30E-09
vg0400676401 sf0400675400 4 676401 NA 1.45E-07
vg0400676505 sf0400675504 4 676505 NA 2.03E-07
vg0124625672 sf0124624628 1 24625672 NA 2.94E-07
vg0528743315 sf0528680670 5 28743315 NA 1.63E-06
vg0222340888 sf0222335019 2 22340888 NA 1.78E-06
vg0433661338 sf0433476221 4 33661338 NA 1.85E-06
vg0708109465 sf0708108470 7 8109465 NA 3.61E-06
vg0221875581 sf0221869712 2 21875581 NA 4.44E-06
vg0402111832 sf0402107426 4 2111832 NA 4.70E-06
vg0619396044 sf0619395047 6 19396044 NA 5.27E-06