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 mr1631 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
vg0405532107 sf0405527548 4 5532107 1.07E-53 3.64E-22
vg0405534646 sf0405530087 4 5534646 1.76E-53 2.22E-22
vg0411120101 sf0411110802 4 11120101 5.04E-39 1.31E-08
vg0410985561 sf0410976262 4 10985561 6.61E-38 1.43E-09
vg0805209310 sf0805208313 8 5209310 2.92E-34 9.41E-09
vg0723279898 sf0723278905 7 23279898 5.32E-34 NA
vg0805194471 sf0805193474 8 5194471 5.83E-34 8.30E-09
vg0302819004 sf0302818000 3 2819004 6.86E-34 NA
vg0405603570 sf0405599011 4 5603570 NA 1.43E-17
vg0405571324 sf0405566765 4 5571324 NA 4.14E-17
vg0405540593 sf0405536034 4 5540593 NA 1.15E-14
vg0405717712 sf0405713151 4 5717712 NA 1.63E-09
vg0409425501 sf0409416200 4 9425501 NA 1.69E-09
vg0405157732 sf0405153174 4 5157732 NA 8.58E-09
vg0411823300 sf0411814011 4 11823300 NA 1.11E-08
vg0326477186 sf0326470280 3 26477186 NA 2.10E-08
vg0409232620 sf0409227893 4 9232620 NA 6.32E-08
vg0405271343 sf0405266784 4 5271343 NA 2.51E-07
vg0400996262 sf0400991814 4 996262 NA 2.78E-07
vg0434000737 sf0433815630 4 34000737 NA 2.82E-07
vg0405141588 sf0405137030 4 5141588 NA 3.01E-07
vg0703625452 sf0703624453 7 3625452 NA 3.58E-07
vg0406038377 sf0406033816 4 6038377 NA 6.00E-07
vg0434065698 sf0433880590 4 34065698 NA 8.58E-07
vg0805209698 sf0805208701 8 5209698 NA 8.98E-07
vg0136199233 sf0136198190 1 36199233 NA 1.16E-06
vg0405232290 sf0405227731 4 5232290 NA 1.22E-06
vg0722241548 sf0722240555 7 22241548 NA 1.47E-06
vg0405251476 sf0405246917 4 5251476 NA 1.67E-06
vg0606463096 sf0606462097 6 6463096 NA 1.71E-06
vg0710376386 sf0710375392 7 10376386 NA 1.87E-06
vg0406792377 sf0406787822 4 6792377 NA 2.04E-06
vg0400676401 sf0400675400 4 676401 NA 2.78E-06
vg0112878686 sf0112877660 1 12878686 NA 3.68E-06
vg0405271834 sf0405267275 4 5271834 NA 4.01E-06