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 mr1255 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
vg0216800422 sf0216794552 2 16800422 2.83E-71 1.00E-30
vg0217021136 sf0217015266 2 17021136 2.97E-65 3.77E-31
vg0900336799 sf0900335799 9 336799 8.79E-35 2.53E-11
vg0900337327 sf0900336327 9 337327 1.06E-34 7.35E-12
vg0213525745 sf0213525741 2 13525745 1.37E-34 5.83E-09
vg1114473442 sf1114009759 11 14473442 2.48E-32 1.20E-08
vg0216474066 sf0216468196 2 16474066 2.05E-31 4.10E-11
vg0216889955 sf0216884085 2 16889955 4.30E-28 4.43E-10
vg0217137640 sf0217131770 2 17137640 1.29E-24 3.16E-06
vg0210764657 sf0210764655 2 10764657 3.35E-24 1.20E-08
vg0210766159 sf0210766157 2 10766159 3.32E-23 1.19E-08
vg0210017956 sf0210017954 2 10017956 1.53E-22 3.58E-06
vg0525795709 sf0525733130 5 25795709 8.45E-22 NA
vg1219227451 sf1219198921 12 19227451 8.68E-22 3.73E-06
vg0217232931 sf0217227061 2 17232931 NA 2.69E-19
vg0217327456 sf0217321586 2 17327456 NA 3.93E-09
vg0217270732 sf0217264862 2 17270732 NA 3.98E-09
vg0216382990 sf0216377120 2 16382990 NA 9.83E-09
vg1121625049 sf1121158926 11 21625049 NA 4.66E-08
vg1005364864 sf1005381401 10 5364864 NA 6.00E-08
vg0216821215 sf0216815345 2 16821215 NA 9.78E-08
vg1216729378 sf1216723332 12 16729378 NA 1.12E-07
vg1213797573 sf1213794911 12 13797573 NA 1.86E-07
vg0210480404 sf0210480402 2 10480404 NA 5.80E-07
vg0815304114 sf0815301400 8 15304114 NA 1.17E-06
vg0611109671 sf0611108672 6 11109671 NA 1.48E-06
vg0610125469 sf0610124470 6 10125469 NA 3.35E-06