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 mr1087 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
vg0610642844 sf0610641845 6 10642844 4.06E-114 9.32E-44
vg0617614534 sf0617613537 6 17614534 1.82E-65 2.74E-07
vg0617821393 sf0617820396 6 17821393 4.83E-64 3.60E-09
vg0717187878 sf0717186885 7 17187878 7.49E-64 NA
vg0705606178 sf0705605179 7 5606178 1.39E-62 NA
vg0613854532 sf0613853533 6 13854532 7.63E-62 1.41E-07
vg0610679715 sf0610678716 6 10679715 NA 2.07E-27
vg0610476027 sf0610475028 6 10476027 NA 4.67E-17
vg0610763769 sf0610762770 6 10763769 NA 4.89E-17
vg0610422329 sf0610421330 6 10422329 NA 2.82E-11
vg0610151699 sf0610150700 6 10151699 NA 8.06E-10
vg0610443927 sf0610442928 6 10443927 NA 8.32E-10
vg0611127099 sf0611126100 6 11127099 NA 1.26E-09
vg0610886230 sf0610885231 6 10886230 NA 2.98E-09
vg0610393322 sf0610392323 6 10393322 NA 1.05E-08
vg0609930953 sf0609929954 6 9930953 NA 2.22E-08
vg0610634160 sf0610633161 6 10634160 NA 4.18E-08
vg0610546081 sf0610545082 6 10546081 NA 4.20E-08
vg0610102601 sf0610101602 6 10102601 NA 7.81E-08
vg0611845202 sf0611856608 6 11845202 NA 1.14E-07
vg0610394969 sf0610393970 6 10394969 NA 3.26E-07
vg0209835682 sf0209835680 2 9835682 NA 3.73E-07
vg0715849539 sf0715848546 7 15849539 NA 4.25E-07
vg0618030192 sf0618029195 6 18030192 NA 8.17E-07
vg0609903615 sf0609902616 6 9903615 NA 1.47E-06
vg0609867319 sf0609866320 6 9867319 NA 1.64E-06
vg0610852431 sf0610851432 6 10852431 NA 2.23E-06