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 mr1390 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
vg1215968758 sf1215966054 12 15968758 5.43E-74 7.05E-34
vg1209571445 sf1209568854 12 9571445 4.71E-54 2.52E-20
vg1210300519 sf1210297932 12 10300519 2.76E-50 1.11E-24
vg1223872806 sf1223839259 12 23872806 4.71E-42 2.30E-08
vg1212726422 sf1212723761 12 12726422 3.97E-26 1.42E-06
vg1212938220 sf1212935559 12 12938220 6.53E-26 4.39E-07
vg0410423427 sf0410414126 4 10423427 3.40E-23 7.83E-06
vg1223876846 sf1223843299 12 23876846 1.39E-20 1.06E-09
vg1215956423 sf1215953719 12 15956423 2.04E-17 7.41E-09
vg0217462869 sf0217456999 2 17462869 6.94E-17 1.07E-06
vg1216192507 sf1216189803 12 16192507 3.82E-15 1.88E-10
vg1216058405 sf1216055701 12 16058405 4.57E-15 6.92E-07
vg0315452372 sf0315451019 3 15452372 3.40E-14 1.17E-06
vg0317164649 sf0317163459 3 17164649 9.10E-14 1.26E-06
vg0526374847 sf0526312210 5 26374847 9.46E-14 1.58E-06
vg1207570300 sf1207567705 12 7570300 1.22E-13 2.16E-11
vg1214847524 sf1214844865 12 14847524 1.51E-12 3.02E-10
vg1210429306 sf1210426719 12 10429306 2.85E-12 6.86E-07
vg1215975684 sf1215972980 12 15975684 3.45E-12 9.13E-07
vg1214706284 sf1214703625 12 14706284 2.01E-11 9.67E-07
vg1217055950 sf1217049905 12 17055950 2.22E-11 1.19E-07
vg1114869295 sf1114405609 11 14869295 NA 6.88E-07
vg1216278958 sf1216276254 12 16278958 NA 8.74E-07
vg1217104604 sf1217098559 12 17104604 NA 1.56E-06