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 mr1016 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
vg1215854444 sf1215851740 12 15854444 1.40E-80 5.32E-36
vg1215854989 sf1215852285 12 15854989 2.74E-80 3.49E-36
vg1209571445 sf1209568854 12 9571445 3.37E-62 2.01E-24
vg1223872806 sf1223839259 12 23872806 1.89E-44 3.40E-08
vg1223873419 sf1223839872 12 23873419 4.81E-38 7.72E-10
vg1212726422 sf1212723761 12 12726422 3.17E-29 9.04E-08
vg1212938220 sf1212935559 12 12938220 2.07E-27 1.58E-10
vg0410423427 sf0410414126 4 10423427 2.31E-24 2.15E-06
vg1212129784 sf1212127120 12 12129784 3.41E-20 7.97E-08
vg0217462843 sf0217456973 2 17462843 8.14E-19 3.48E-07
vg0408294814 sf0408290088 4 8294814 4.03E-18 1.14E-07
vg1207827697 sf1207825103 12 7827697 1.93E-17 1.11E-12
vg0526374490 sf0526311853 5 26374490 1.11E-16 7.58E-08
vg1216192507 sf1216189803 12 16192507 1.41E-15 3.87E-10
vg1215983666 sf1215980962 12 15983666 1.97E-15 4.00E-07
vg1216282451 sf1216279747 12 16282451 4.26E-14 6.62E-07
vg0317365562 sf0317364372 3 17365562 1.62E-13 3.46E-07
vg1214847524 sf1214844865 12 14847524 2.07E-13 3.61E-11
vg1215975684 sf1215972980 12 15975684 7.14E-12 1.27E-07
vg1216278238 sf1216275534 12 16278238 NA 1.04E-09
vg0912501909 sf0912500908 9 12501909 NA 1.48E-07
vg0408380913 sf0408376187 4 8380913 NA 1.90E-07
vg1216542145 sf1216539438 12 16542145 NA 4.46E-07
vg1209049562 sf1209046971 12 9049562 NA 1.04E-06