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 mr1244 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
vg0610487064 sf0610486065 6 10487064 9.83E-40 9.58E-14
vg0402394297 sf0402389892 4 2394297 2.72E-30 NA
vg0719256109 sf0719255116 7 19256109 5.54E-30 NA
vg0122402967 sf0122401922 1 22402967 8.39E-29 NA
vg0719345309 sf0719344316 7 19345309 1.05E-28 NA
vg0130351635 sf0130350591 1 30351635 6.54E-28 2.68E-06
vg0505543319 sf0505543257 5 5543319 2.64E-25 2.65E-06
vg0520363169 sf0520300642 5 20363169 4.54E-23 2.33E-08
vg0508659205 sf0508659133 5 8659205 1.10E-22 1.57E-06
vg0123784103 sf0123783059 1 23784103 2.94E-22 1.12E-07
vg0610587682 sf0610586683 6 10587682 NA 9.33E-10
vg0920309427 sf0920308946 9 20309427 NA 3.44E-09
vg0920307510 sf0920307029 9 20307510 NA 2.54E-07
vg1219427349 sf1219398819 12 19427349 NA 4.08E-07
vg0314502491 sf0314501179 3 14502491 NA 4.17E-07
vg0611989326 sf0611988327 6 11989326 NA 8.76E-07
vg0609926030 sf0609925031 6 9926030 NA 1.36E-06
vg1115723826 sf1115260135 11 15723826 NA 2.08E-06
vg1115403686 sf1114939998 11 15403686 NA 3.99E-06
vg0610285178 sf0610284179 6 10285178 NA 4.96E-06
vg0627037652 sf0627036655 6 27037652 NA 8.47E-06