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 mr1336 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
vg0142045683 sf0142044640 1 42045683 3.81E-10 4.58E-07
vg0601643650 sf0601642651 6 1643650 1.27E-09 3.66E-06
vg0104006648 sf0104005648 1 4006648 1.28E-09 8.18E-07
vg0104078758 sf0104077758 1 4078758 1.32E-09 2.31E-07
vg0817080070 sf0817077356 8 17080070 2.25E-09 NA
vg1105495945 sf1105491696 11 5495945 6.03E-09 8.35E-07
vg0601508115 sf0601507116 6 1508115 1.35E-08 1.30E-06
vg0601514136 sf0601513137 6 1514136 2.26E-08 4.37E-06
vg1217549799 sf1217543754 12 17549799 3.11E-08 1.00E-06
vg1200180642 sf1200179642 12 180642 6.43E-08 2.25E-06
vg0728914146 sf0728913154 7 28914146 8.48E-07 4.50E-06
vg0907855221 sf0907854221 9 7855221 2.56E-06 NA
vg1121600548 sf1121134425 11 21600548 4.22E-06 1.68E-06
vg0729024509 sf0729023517 7 29024509 5.80E-06 NA
vg1222483382 sf1222449821 12 22483382 NA 3.83E-06