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 mr1234 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
vg0610559165 sf0610558166 6 10559165 1.04E-51 1.90E-36
vg0610584498 sf0610583499 6 10584498 5.07E-39 3.92E-26
vg0610412338 sf0610411339 6 10412338 4.14E-33 3.22E-18
vg0610679624 sf0610678625 6 10679624 6.37E-24 7.08E-21
vg0617319066 sf0617318069 6 17319066 1.36E-19 1.08E-06
vg0610872827 sf0610871828 6 10872827 7.71E-18 1.03E-06
vg0610846322 sf0610845323 6 10846322 4.49E-17 8.53E-11
vg0610147528 sf0610146529 6 10147528 1.40E-16 3.08E-09
vg0610150248 sf0610149249 6 10150248 1.03E-13 5.44E-12
vg0613057898 sf0613056899 6 13057898 2.92E-13 4.40E-08
vg0617595576 sf0617594579 6 17595576 5.78E-13 6.78E-08
vg0610488879 sf0610487880 6 10488879 3.85E-12 6.09E-08
vg0611470898 sf0611469899 6 11470898 5.70E-12 1.43E-07
vg0614543893 sf0614542894 6 14543893 9.06E-12 7.55E-07
vg0612056790 sf0612055791 6 12056790 5.27E-11 1.23E-08
vg0610442142 sf0610441143 6 10442142 1.28E-10 3.19E-12
vg0611638449 sf0611637450 6 11638449 2.83E-10 2.65E-11
vg0610127588 sf0610126589 6 10127588 NA 8.24E-12
vg0617876285 sf0617875288 6 17876285 NA 3.25E-08
vg0610752419 sf0610751420 6 10752419 NA 5.84E-08
vg0609215660 sf0609214661 6 9215660 NA 5.54E-07
vg0515926609 sf0515869116 5 15926609 NA 5.65E-07
vg0610611540 sf0610610541 6 10611540 NA 9.23E-07
vg0223043170 sf0223037301 2 23043170 NA 3.33E-06