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 mr1533 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
vg1013533412 sf1013462182 10 13533412 2.69E-83 2.40E-41
vg0106949505 sf0106948505 1 6949505 1.00E-42 NA
vg0800110381 sf0800109381 8 110381 9.96E-41 NA
vg0129926022 sf0129924977 1 29926022 1.91E-40 NA
vg0311216012 sf0311214730 3 11216012 2.99E-40 NA
vg1013528182 sf1013456952 10 13528182 NA 7.37E-24
vg1013392907 sf1013321677 10 13392907 NA 2.36E-14
vg1013277170 sf1013205939 10 13277170 NA 1.55E-12
vg1013393741 sf1013322511 10 13393741 NA 8.95E-12
vg1013634835 sf1013563604 10 13634835 NA 2.51E-09
vg1013156252 sf1013085023 10 13156252 NA 1.09E-08
vg0817676420 sf0817673707 8 17676420 NA 1.59E-07
vg1013680813 sf1013609582 10 13680813 NA 2.00E-07
vg0917270003 sf0917269002 9 17270003 NA 3.68E-07
vg0818051811 sf0818049098 8 18051811 NA 4.44E-07
vg1013475468 sf1013404238 10 13475468 NA 1.44E-06
vg1013801258 sf1013730027 10 13801258 NA 2.86E-06
vg1119383363 sf1118917051 11 19383363 NA 2.97E-06
vg1013347408 sf1013276178 10 13347408 NA 3.53E-06
vg1013422858 sf1013351628 10 13422858 NA 4.15E-06
vg0110864670 sf0110863646 1 10864670 NA 4.44E-06