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 mr1918 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
vg0222743508 sf0222737639 2 22743508 1.34E-57 1.40E-49
vg0222723992 sf0222718123 2 22723992 1.67E-56 4.23E-50
vg0222725003 sf0222719134 2 22725003 1.82E-38 3.80E-21
vg0229743646 sf0229737777 2 29743646 9.39E-19 NA
vg0130110476 sf0130109431 1 30110476 2.38E-18 NA
vg0104077013 sf0104076013 1 4077013 4.44E-18 NA
vg0224878279 sf0224872410 2 24878279 6.40E-16 1.49E-07
vg0224233343 sf0224227474 2 24233343 1.88E-13 8.63E-09
vg0222729132 sf0222723263 2 22729132 4.75E-13 1.49E-07
vg0222681985 sf0222676116 2 22681985 1.17E-12 2.36E-13
vg0222041029 sf0222035160 2 22041029 3.90E-12 3.53E-08
vg0223742023 sf0223736154 2 23742023 NA 8.92E-12
vg0224832469 sf0224826600 2 24832469 NA 6.08E-09
vg0223663745 sf0223657876 2 23663745 NA 6.17E-09
vg0224676560 sf0224670691 2 24676560 NA 2.18E-07
vg0222857256 sf0222851387 2 22857256 NA 3.17E-07
vg0222634177 sf0222628308 2 22634177 NA 3.73E-07
vg0222799084 sf0222793215 2 22799084 NA 1.01E-06
vg0525239875 sf0525177296 5 25239875 NA 1.38E-06
vg0221566997 sf0221561128 2 21566997 NA 1.57E-06
vg1112606104 sf1112142307 11 12606104 NA 2.18E-06
vg0218580570 sf0218574701 2 18580570 NA 2.20E-06
vg1204287881 sf1204286869 12 4287881 NA 2.50E-06
vg0221483879 sf0221478010 2 21483879 NA 3.55E-06