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 mr1952 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
vg0904129441 sf0904128441 9 4129441 1.24E-08 4.65E-06
vg0213595540 sf0213595536 2 13595540 1.80E-08 NA
vg0513679034 sf0513621580 5 13679034 2.38E-08 NA
vg0520021683 sf0519959159 5 20021683 6.73E-08 NA
vg1006277345 sf1006292968 10 6277345 6.93E-08 NA
vg0727529849 sf0727528855 7 27529849 9.82E-08 1.15E-06
vg0527800386 sf0527737743 5 27800386 3.35E-06 NA
vg1017358348 sf1017287121 10 17358348 NA 5.85E-07
vg1208192471 sf1208189877 12 8192471 NA 6.21E-06