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 mr1559 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
vg0325696417 sf0325694435 3 25696417 8.05E-14 2.86E-14
vg1005318536 sf1005335073 10 5318536 8.71E-10 5.97E-07
vg1004077040 sf1004076016 10 4077040 1.96E-09 NA
vg0400345487 sf0400344487 4 345487 3.27E-09 5.02E-08
vg1004081061 sf1004080037 10 4081061 5.26E-09 4.42E-06
vg1010974062 sf1010902882 10 10974062 5.45E-09 3.33E-08
vg1004546341 sf1004562879 10 4546341 1.78E-08 9.71E-07
vg1010999956 sf1010928776 10 10999956 2.17E-08 3.29E-06
vg0202749886 sf0202749884 2 2749886 2.69E-08 1.67E-06
vg0609926305 sf0609925306 6 9926305 3.76E-08 4.11E-07
vg1107093285 sf1107089030 11 7093285 2.42E-07 7.17E-08
vg0322366031 sf0322364520 3 22366031 2.79E-07 4.35E-07
vg1121959877 sf1121493748 11 21959877 2.98E-07 1.36E-06
vg0317037478 sf0317036352 3 17037478 3.07E-07 3.07E-07
vg0625912245 sf0625911248 6 25912245 5.33E-07 1.26E-06
vg0227533021 sf0227527152 2 27533021 5.67E-07 2.65E-06
vg0708919428 sf0708918434 7 8919428 7.96E-07 NA
vg0333517525 sf0333510395 3 33517525 9.47E-07 3.10E-06
vg1005619377 sf1005635915 10 5619377 4.08E-06 2.11E-06