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 mr1218 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
vg0610487469 sf0610486470 6 10487469 4.34E-50 1.70E-17
vg0612996928 sf0612995929 6 12996928 5.89E-32 NA
vg0617359224 sf0617358227 6 17359224 4.56E-31 NA
vg0616890329 sf0616889332 6 16890329 2.78E-29 8.63E-08
vg0629122299 sf0629121301 6 29122299 3.27E-25 NA
vg0719242566 sf0719241573 7 19242566 7.52E-25 NA
vg0610788671 sf0610787672 6 10788671 4.76E-19 2.57E-08
vg0610590324 sf0610589325 6 10590324 4.79E-19 9.21E-07
vg0610596670 sf0610595671 6 10596670 NA 5.14E-11
vg0610787522 sf0610786523 6 10787522 NA 9.05E-10
vg0610114266 sf0610113267 6 10114266 NA 3.67E-09
vg0611735326 sf0611734327 6 11735326 NA 1.07E-08
vg0610438538 sf0610437539 6 10438538 NA 6.22E-08
vg0616948087 sf0616947090 6 16948087 NA 1.21E-07
vg0610886230 sf0610885231 6 10886230 NA 1.52E-07
vg0610061410 sf0610060411 6 10061410 NA 2.46E-07
vg1214802798 sf1214800139 12 14802798 NA 1.06E-06
vg0610181986 sf0610180987 6 10181986 NA 1.16E-06
vg0502139452 sf0502139426 5 2139452 NA 1.28E-06
vg0719290633 sf0719289640 7 19290633 NA 2.03E-06
vg0611990477 sf0611989478 6 11990477 NA 3.75E-06
vg0728892745 sf0728891753 7 28892745 NA 4.23E-06
vg0611081410 sf0611080411 6 11081410 NA 4.83E-06
vg0513901793 sf0513844337 5 13901793 NA 8.93E-06