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 mr1962 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
vg0222746050 sf0222740181 2 22746050 1.28E-92 2.63E-27
vg0222727819 sf0222721950 2 22727819 4.13E-92 8.59E-28
vg0406395970 sf0406391410 4 6395970 7.28E-72 2.88E-07
vg0406561841 sf0406557284 4 6561841 1.14E-70 1.27E-08
vg0705306490 sf0705305491 7 5306490 2.99E-70 4.14E-06
vg0406097513 sf0406092952 4 6097513 5.74E-70 3.99E-09
vg0626745994 sf0626744997 6 26745994 1.40E-67 NA
vg0412427420 sf0412418134 4 12427420 2.94E-67 NA
vg0916685790 sf0916684789 9 16685790 1.12E-63 4.26E-06
vg0614107939 sf0614106940 6 14107939 1.20E-62 1.29E-07
vg0223721789 sf0223715920 2 23721789 NA 1.71E-11
vg0222573327 sf0222567458 2 22573327 NA 9.62E-11
vg0222725003 sf0222719134 2 22725003 NA 4.53E-09
vg0222857256 sf0222851387 2 22857256 NA 2.32E-08
vg0223720133 sf0223714264 2 23720133 NA 2.22E-07
vg0122332434 sf0122331389 1 22332434 NA 4.81E-07
vg0222633552 sf0222627683 2 22633552 NA 6.61E-07
vg0222729853 sf0222723984 2 22729853 NA 1.02E-06
vg0209234495 sf0209234493 2 9234495 NA 1.05E-06
vg0122469340 sf0122468295 1 22469340 NA 1.99E-06
vg0223023400 sf0223017531 2 23023400 NA 2.94E-06
vg0222817468 sf0222811599 2 22817468 NA 3.05E-06
vg0224242820 sf0224236951 2 24242820 NA 3.28E-06
vg0222729132 sf0222723263 2 22729132 NA 3.75E-06
vg1020291609 sf1020220089 10 20291609 NA 3.95E-06
vg0717362404 sf0717361411 7 17362404 NA 4.13E-06
vg0311534838 sf0311533556 3 11534838 NA 4.93E-06