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 mr1310 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
vg1000757961 sf1000756937 10 757961 1.92E-21 4.62E-14
vg0528146502 sf0528083857 5 28146502 6.50E-13 9.71E-08
vg0700359527 sf0700358527 7 359527 5.30E-12 2.11E-07
vg1008205459 sf1008134321 10 8205459 1.07E-11 1.28E-06
vg1008206965 sf1008135827 10 8206965 1.56E-11 1.19E-06
vg1128801387 sf1128278166 11 28801387 2.52E-11 2.81E-06
vg1128842480 sf1128319259 11 28842480 6.06E-11 2.15E-06
vg1128788765 sf1128265544 11 28788765 9.55E-11 4.95E-07
vg1119999188 sf1119533111 11 19999188 5.07E-09 1.13E-06
vg1125113390 sf1124647230 11 25113390 1.73E-07 5.87E-07
vg1125090609 sf1124624449 11 25090609 NA 1.94E-10
vg1125117714 sf1124651554 11 25117714 NA 4.75E-09
vg0327535213 sf0327528266 3 27535213 NA 1.92E-06
vg1004777607 sf1004794144 10 4777607 NA 4.90E-06