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 mr1200 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
vg1123394093 sf1122927963 11 23394093 6.17E-09 6.17E-09
vg1004567845 sf1004584383 10 4567845 2.67E-08 2.67E-08
vg0124089174 sf0124088130 1 24089174 3.63E-08 3.63E-08
vg0432345183 sf0432160072 4 32345183 4.22E-08 4.22E-08
vg1004596366 sf1004612904 10 4596366 7.17E-08 7.16E-08
vg0916734760 sf0916733759 9 16734760 7.33E-08 7.33E-08
vg0910545581 sf0910544580 9 10545581 1.28E-07 1.28E-07
vg0300180852 sf0300179852 3 180852 1.48E-07 1.48E-07
vg0721054102 sf0721053109 7 21054102 1.71E-07 1.71E-07
vg0727091375 sf0727090381 7 27091375 2.17E-07 2.17E-07
vg0907048512 sf0907047512 9 7048512 2.75E-07 2.75E-07
vg0118080333 sf0118079287 1 18080333 2.95E-07 2.95E-07
vg1214973379 sf1214970721 12 14973379 3.08E-07 3.08E-07
vg0910828660 sf0910827659 9 10828660 4.88E-07 4.88E-07
vg0220950949 sf0220945081 2 20950949 8.26E-07 8.26E-07
vg1220059260 sf1220030702 12 20059260 8.65E-07 8.65E-07
vg0819861761 sf0819859048 8 19861761 8.80E-07 8.80E-07
vg0904368564 sf0904367564 9 4368564 9.75E-07 9.75E-07
vg1126981130 sf1126509517 11 26981130 1.18E-06 1.18E-06
vg0104815238 sf0104814238 1 4815238 1.35E-06 1.35E-06
vg0706185604 sf0706184605 7 6185604 2.09E-06 2.09E-06