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 mr1174 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
vg0429947446 sf0429762313 4 29947446 1.94E-29 1.13E-13
vg0429950282 sf0429765149 4 29950282 4.28E-29 1.11E-13
vg0429954830 sf0429769697 4 29954830 4.71E-29 7.00E-14
vg0804315269 sf0804314272 8 4315269 1.03E-18 8.10E-18
vg0102812041 sf0102811041 1 2812041 1.74E-13 NA
vg0430036961 sf0429851832 4 30036961 5.37E-13 1.63E-07
vg0427020936 sf0426835809 4 27020936 6.34E-13 NA
vg0430035048 sf0429849919 4 30035048 1.36E-11 8.91E-08
vg1207208550 sf1207205944 12 7208550 3.41E-10 NA
vg1217121268 sf1217115223 12 17121268 3.80E-09 1.63E-06
vg0705623945 sf0705622946 7 5623945 6.99E-09 4.22E-06
vg0804327523 sf0804326526 8 4327523 4.02E-08 9.50E-19
vg0429750926 sf0429565795 4 29750926 NA 9.42E-08
vg0220016136 sf0220010268 2 20016136 NA 4.76E-07
vg0804346844 sf0804345847 8 4346844 NA 7.89E-07
vg1215881162 sf1215878458 12 15881162 NA 1.56E-06
vg0727788464 sf0727787471 7 27788464 NA 1.72E-06
vg1127978095 sf1127506481 11 27978095 NA 1.91E-06
vg0727793768 sf0727792775 7 27793768 NA 2.07E-06
vg0310642600 sf0310641516 3 10642600 NA 3.39E-06
vg0401152863 sf0401148413 4 1152863 NA 4.98E-06