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 mr1150 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
vg1127529196 sf1127057583 11 27529196 2.23E-10 2.12E-07
vg0628759426 sf0628758428 6 28759426 3.20E-09 6.97E-07
vg0222833455 sf0222827586 2 22833455 4.63E-09 1.95E-07
vg0609746842 sf0609745843 6 9746842 1.46E-08 1.53E-06
vg0402179876 sf0402175471 4 2179876 1.92E-08 NA
vg0421390453 sf0421218506 4 21390453 2.04E-08 1.94E-06
vg1221097233 sf1221063783 12 21097233 3.51E-08 1.24E-07
vg0221025908 sf0221020040 2 21025908 4.02E-08 8.20E-08
vg0920644583 sf0920644102 9 20644583 1.25E-07 1.06E-08
vg0727090466 sf0727089472 7 27090466 3.82E-07 1.08E-06
vg0502074204 sf0502074186 5 2074204 6.14E-07 3.93E-07
vg0432880368 sf0432695255 4 32880368 3.64E-06 1.75E-06
vg0712392714 sf0712391721 7 12392714 3.64E-06 6.08E-08
vg0905898979 sf0905897979 9 5898979 8.03E-06 8.80E-06
vg0901498790 sf0901497790 9 1498790 NA 2.27E-07
vg0316626378 sf0316625023 3 16626378 NA 5.54E-07
vg1214613948 sf1214611288 12 14613948 NA 6.91E-07
vg0609030568 sf0609029569 6 9030568 NA 1.07E-06
vg1118461468 sf1117995327 11 18461468 NA 2.53E-06
vg1125482367 sf1125016206 11 25482367 NA 2.99E-06
vg0400034044 sf0400033044 4 34044 NA 3.86E-06
vg1109421335 sf1109415912 11 9421335 NA 3.87E-06
vg0208050121 sf0208050120 2 8050121 NA 7.08E-06