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 mr1124 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
vg0222742213 sf0222736344 2 22742213 3.61E-74 2.08E-30
vg0222718166 sf0222712297 2 22718166 1.37E-73 1.17E-30
vg0705626976 sf0705625977 7 5626976 2.08E-47 NA
vg0626805557 sf0626804560 6 26805557 1.24E-45 NA
vg0304989522 sf0304988524 3 4989522 2.98E-43 NA
vg0521767607 sf0521705049 5 21767607 4.84E-43 NA
vg0222725003 sf0222719134 2 22725003 NA 1.74E-13
vg0223721789 sf0223715920 2 23721789 NA 2.22E-11
vg0222630367 sf0222624498 2 22630367 NA 4.45E-07
vg0223663745 sf0223657876 2 23663745 NA 7.12E-07
vg0223720122 sf0223714253 2 23720122 NA 9.24E-07
vg0610566738 sf0610565739 6 10566738 NA 1.09E-06
vg1224760800 sf1224727254 12 24760800 NA 2.10E-06
vg0222817468 sf0222811599 2 22817468 NA 2.44E-06
vg0820942801 sf0820940088 8 20942801 NA 2.88E-06
vg0224573690 sf0224567821 2 24573690 NA 3.09E-06
vg0917488027 sf0917487026 9 17488027 NA 3.37E-06
vg0311437556 sf0311436274 3 11437556 NA 3.82E-06
vg1112606104 sf1112142307 11 12606104 NA 4.95E-06
vg1122792828 sf1122326699 11 22792828 NA 5.82E-06