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 mr1865 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
vg0922450232 sf0922449751 9 22450232 8.70E-29 3.12E-21
vg0922500002 sf0922499521 9 22500002 5.64E-27 5.57E-24
vg0922419033 sf0922418552 9 22419033 1.89E-17 6.12E-16
vg0922421758 sf0922421277 9 22421758 4.30E-16 4.38E-15
vg0922595826 sf0922595345 9 22595826 1.37E-15 3.89E-13
vg0922383096 sf0922382615 9 22383096 2.24E-15 1.32E-14
vg0922187192 sf0922186711 9 22187192 1.86E-12 6.26E-12
vg0922210878 sf0922210397 9 22210878 3.78E-12 2.85E-10
vg0922253697 sf0922253216 9 22253697 2.61E-09 1.18E-11
vg0606702965 sf0606701966 6 6702965 1.75E-08 1.28E-06
vg0922436614 sf0922436133 9 22436614 2.10E-08 3.57E-06
vg0519406969 sf0519344453 5 19406969 5.03E-08 8.59E-07
vg0922486287 sf0922485806 9 22486287 1.20E-07 8.67E-07
vg0922661467 sf0922660986 9 22661467 3.00E-07 1.26E-06
vg0922435973 sf0922435492 9 22435973 2.31E-06 3.74E-06
vg0224011069 sf0224005200 2 24011069 5.57E-06 1.10E-06
vg0922863463 sf0922862982 9 22863463 8.53E-06 2.34E-06
vg0922731162 sf0922730681 9 22731162 9.37E-06 7.03E-08
vg0406706405 sf0406701852 4 6706405 NA 5.29E-07