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 mr1800 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
vg0432523372 sf0432338264 4 32523372 1.02E-16 4.83E-12
vg0432630242 sf0432445131 4 32630242 1.75E-16 1.59E-11
vg0125786178 sf0125785134 1 25786178 2.70E-14 2.48E-08
vg1018943301 sf1018871858 10 18943301 3.62E-14 1.77E-07
vg0700837076 sf0700836076 7 837076 2.03E-13 1.14E-08
vg0231389934 sf0231384065 2 31389934 5.18E-13 5.14E-07
vg0318195210 sf0318193992 3 18195210 1.15E-12 2.60E-09
vg0406525139 sf0406520582 4 6525139 2.19E-12 1.70E-07
vg1018945910 sf1018874467 10 18945910 2.47E-12 NA
vg0803690368 sf0803689371 8 3690368 2.78E-12 2.64E-08
vg0408107056 sf0408102330 4 8107056 3.21E-12 3.43E-08
vg0816279098 sf0816276384 8 16279098 8.69E-12 2.17E-07
vg0708118551 sf0708117556 7 8118551 2.22E-11 1.58E-06
vg0713426232 sf0713425239 7 13426232 5.48E-11 2.10E-06
vg0311861697 sf0311860415 3 11861697 7.36E-11 1.04E-07
vg0138794828 sf0138793785 1 38794828 1.75E-10 1.57E-06
vg0910025779 sf0910024778 9 10025779 2.10E-10 1.80E-06
vg0105865757 sf0105864757 1 5865757 5.30E-10 8.46E-07
vg0418308850 sf0418136896 4 18308850 3.15E-09 4.86E-07
vg0408073934 sf0408069208 4 8073934 4.52E-09 NA
vg0805068327 sf0805067330 8 5068327 1.14E-08 1.39E-06
vg0432568737 sf0432383628 4 32568737 NA 1.19E-07
vg1006743978 sf1006759601 10 6743978 NA 2.23E-07
vg1225422871 sf1225389267 12 25422871 NA 2.36E-07
vg0207810055 sf0207810054 2 7810055 NA 1.04E-06
vg0619177386 sf0619176389 6 19177386 NA 1.29E-06
vg0910357999 sf0910356998 9 10357999 NA 1.30E-06
vg0431599339 sf0431414234 4 31599339 NA 1.42E-06
vg0432524793 sf0432339685 4 32524793 NA 2.51E-06
vg0915672813 sf0915671812 9 15672813 NA 4.02E-06