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 mr1111 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
vg0610608095 sf0610607096 6 10608095 6.11E-41 1.06E-24
vg0610566084 sf0610565085 6 10566084 1.76E-40 9.98E-26
vg0610684751 sf0610683752 6 10684751 3.04E-14 6.02E-08
vg0402394297 sf0402389892 4 2394297 1.55E-12 NA
vg0610435285 sf0610434286 6 10435285 3.65E-12 2.77E-09
vg0920307704 sf0920307223 9 20307704 4.55E-12 NA
vg0610685381 sf0610684382 6 10685381 3.15E-11 3.97E-10
vg0610419183 sf0610418184 6 10419183 3.90E-11 1.28E-11
vg0610752789 sf0610751790 6 10752789 1.43E-10 1.86E-11
vg0617621257 sf0617620260 6 17621257 2.45E-10 2.18E-06
vg0613062563 sf0613061564 6 13062563 1.82E-09 1.09E-06
vg0610613420 sf0610612421 6 10613420 9.03E-09 7.94E-07
vg0610628819 sf0610627820 6 10628819 7.70E-08 3.50E-06
vg0610687475 sf0610686476 6 10687475 7.81E-08 1.30E-08
vg1218724628 sf1218696063 12 18724628 8.53E-08 1.67E-06
vg0617603352 sf0617602355 6 17603352 2.33E-07 1.12E-06
vg0611098102 sf0611097103 6 11098102 2.94E-07 3.55E-07
vg0610772213 sf0610771214 6 10772213 7.03E-07 1.21E-08
vg0611643367 sf0611642368 6 11643367 1.40E-06 1.19E-06
vg0226057933 sf0226052064 2 26057933 3.28E-06 NA
vg0421592215 sf0421420265 4 21592215 NA 2.41E-06
vg0217387611 sf0217381741 2 17387611 NA 2.64E-06
vg0825168314 sf0825165600 8 25168314 NA 3.05E-06
vg0816239139 sf0816236425 8 16239139 NA 3.48E-06
vg1204397865 sf1204396853 12 4397865 NA 4.47E-06