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 mr1408 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
vg0719041739 sf0719040746 7 19041739 1.33E-17 8.02E-16
vg0428494128 sf0428308982 4 28494128 4.43E-15 1.17E-09
vg0719052758 sf0719051765 7 19052758 1.22E-13 3.52E-16
vg1214192780 sf1214190120 12 14192780 1.50E-11 2.71E-07
vg0218013275 sf0218007406 2 18013275 5.75E-11 NA
vg1200287429 sf1200286429 12 287429 6.31E-11 1.31E-06
vg0218613608 sf0218607739 2 18613608 8.14E-11 4.76E-07
vg0136510873 sf0136509830 1 36510873 2.31E-10 3.04E-07
vg0315318850 sf0315317497 3 15318850 9.66E-10 1.95E-08
vg0719436399 sf0719435406 7 19436399 1.35E-09 2.08E-08
vg1105544417 sf1105540169 11 5544417 1.97E-09 2.62E-07
vg1217507757 sf1217501712 12 17507757 7.14E-09 2.20E-06
vg0407630134 sf0407625401 4 7630134 9.02E-09 NA
vg0719144059 sf0719143066 7 19144059 1.75E-08 1.77E-08
vg0804330490 sf0804329493 8 4330490 2.50E-08 3.60E-07
vg0324882835 sf0324880914 3 24882835 3.56E-08 1.33E-07
vg0719345307 sf0719344314 7 19345307 1.00E-07 3.40E-07
vg0322556933 sf0322555422 3 22556933 1.51E-07 NA
vg0916892004 sf0916891003 9 16892004 2.37E-07 NA
vg0316348941 sf0316347588 3 16348941 9.87E-07 NA
vg0900499731 sf0900498731 9 499731 1.86E-06 2.68E-06
vg0305453341 sf0305452341 3 5453341 2.38E-06 NA
vg0719271739 sf0719270746 7 19271739 NA 8.98E-12
vg0719041118 sf0719040125 7 19041118 NA 2.22E-09
vg0719408893 sf0719407900 7 19408893 NA 7.15E-09
vg1100676096 sf1100675099 11 676096 NA 5.20E-08
vg0719371966 sf0719370973 7 19371966 NA 4.13E-07
vg0317333132 sf0317331942 3 17333132 NA 6.88E-07
vg0329561125 sf0329554165 3 29561125 NA 9.52E-07
vg0218591225 sf0218585356 2 18591225 NA 1.49E-06
vg0424279067 sf0424093928 4 24279067 NA 3.07E-06