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 mr1118 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
vg1005826161 sf1005842699 10 5826161 7.18E-30 9.01E-08
vg1009141969 sf1009070830 10 9141969 2.63E-29 8.37E-08
vg0222673217 sf0222667348 2 22673217 4.00E-27 5.54E-19
vg1009101162 sf1009030023 10 9101162 5.14E-27 4.11E-06
vg1009179985 sf1009108806 10 9179985 1.73E-25 4.28E-07
vg1006082586 sf1006099123 10 6082586 9.22E-24 NA
vg1006851906 sf1006867529 10 6851906 1.23E-23 4.40E-09
vg1216843191 sf1216837145 12 16843191 1.85E-21 7.71E-10
vg1006529969 sf1006545592 10 6529969 1.53E-19 6.17E-10
vg1218624984 sf1218596420 12 18624984 1.64E-18 5.69E-08
vg1009697437 sf1009626258 10 9697437 5.02E-16 1.48E-07
vg0626215270 sf0626214273 6 26215270 8.42E-15 4.00E-07
vg1006839627 sf1006855250 10 6839627 NA 6.90E-14
vg0222722554 sf0222716685 2 22722554 NA 3.37E-11
vg1009708303 sf1009637124 10 9708303 NA 4.49E-11
vg1110436777 sf1110431322 11 10436777 NA 1.78E-08
vg0327037726 sf0327030779 3 27037726 NA 2.97E-08
vg0303412434 sf0303411430 3 3412434 NA 1.01E-07
vg1209215198 sf1209212607 12 9215198 NA 1.60E-07
vg1009653864 sf1009582685 10 9653864 NA 2.10E-07
vg1007190202 sf1007205825 10 7190202 NA 2.24E-07
vg0316147114 sf0316145761 3 16147114 NA 2.76E-07
vg0141599747 sf0141598704 1 41599747 NA 3.04E-07
vg1010093642 sf1010022463 10 10093642 NA 4.50E-07
vg0223710893 sf0223705024 2 23710893 NA 5.39E-07
vg1218466305 sf1218437741 12 18466305 NA 1.16E-06
vg0421291418 sf0421119472 4 21291418 NA 3.99E-06