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 mr1128 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
vg1006197978 sf1006213627 10 6197978 2.15E-14 1.20E-12
vg1008921522 sf1008850383 10 8921522 5.73E-13 4.62E-11
vg0407825281 sf0407820549 4 7825281 2.01E-11 2.62E-09
vg1202805818 sf1202804820 12 2805818 3.58E-09 7.44E-06
vg1009411390 sf1009340211 10 9411390 3.66E-09 3.49E-10
vg0610034444 sf0610033445 6 10034444 3.11E-08 2.48E-06
vg0610752378 sf0610751379 6 10752378 3.68E-08 3.92E-06
vg1121617620 sf1121151497 11 21617620 4.27E-08 5.77E-08
vg0903295768 sf0903294768 9 3295768 6.72E-08 6.27E-07
vg0714251118 sf0714250125 7 14251118 8.33E-08 1.76E-07
vg0235919875 sf0235914006 2 35919875 2.10E-07 3.13E-06
vg0813433527 sf0813431080 8 13433527 6.34E-07 2.85E-06
vg0502440516 sf0502440492 5 2440516 6.47E-07 8.71E-08
vg0412457585 sf0412448300 4 12457585 1.76E-06 2.11E-06
vg0725884668 sf0725883674 7 25884668 2.96E-06 6.51E-07
vg1111172103 sf1111166420 11 11172103 3.25E-06 7.24E-07
vg0432204214 sf0432019106 4 32204214 7.53E-06 3.12E-06
vg1004365897 sf1004382435 10 4365897 NA 3.95E-06
vg0528741746 sf0528679101 5 28741746 NA 4.33E-06
vg1121621866 sf1121155743 11 21621866 NA 8.09E-06