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 mr1443 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
vg0722383200 sf0722382207 7 22383200 3.57E-11 NA
vg1216176111 sf1216173407 12 16176111 4.69E-11 8.12E-06
vg0630760388 sf0630759390 6 30760388 7.16E-11 6.10E-06
vg0203016808 sf0203016806 2 3016808 1.36E-10 NA
vg0102710977 sf0102709977 1 2710977 4.16E-10 NA
vg0826865048 sf0826862334 8 26865048 1.72E-09 3.64E-06
vg1216258965 sf1216256261 12 16258965 2.59E-09 4.05E-06
vg0800643128 sf0800642128 8 643128 6.42E-08 NA
vg1216059532 sf1216056828 12 16059532 1.12E-07 1.77E-06
vg0212843658 sf0212843654 2 12843658 1.24E-07 2.09E-07
vg1218191046 sf1218162482 12 18191046 1.70E-07 1.78E-07
vg0400844895 sf0400843895 4 844895 5.19E-07 NA
vg0107372570 sf0107371570 1 7372570 NA 6.90E-08
vg1209691208 sf1209688617 12 9691208 NA 5.43E-07
vg1016607084 sf1016535857 10 16607084 NA 9.78E-07
vg1209425640 sf1209423049 12 9425640 NA 2.56E-06