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 mr1490 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 2.44E-66 3.66E-31
vg1209571445 sf1209568854 12 9571445 1.77E-49 2.42E-19
vg1210300519 sf1210297932 12 10300519 3.09E-46 7.97E-23
vg1223872806 sf1223839259 12 23872806 1.17E-39 2.43E-09
vg1223877099 sf1223843552 12 23877099 1.53E-29 1.21E-06
vg1212726422 sf1212723761 12 12726422 1.80E-24 2.76E-06
vg1212938220 sf1212935559 12 12938220 2.54E-24 4.67E-07
vg0410423427 sf0410414126 4 10423427 3.34E-21 NA
vg1223876846 sf1223843299 12 23876846 3.50E-20 1.90E-09
vg1209926499 sf1209923909 12 9926499 1.62E-17 1.24E-06
vg1215956423 sf1215953719 12 15956423 2.84E-17 1.10E-08
vg0526374490 sf0526311853 5 26374490 4.92E-16 3.06E-06
vg1216192507 sf1216189803 12 16192507 3.88E-15 1.69E-10
vg0315452372 sf0315451019 3 15452372 2.96E-13 2.52E-06
vg0317164649 sf0317163459 3 17164649 4.56E-13 4.48E-06
vg1207570300 sf1207567705 12 7570300 1.01E-12 2.13E-10
vg1215520105 sf1215517402 12 15520105 4.53E-12 3.33E-07
vg1217055950 sf1217049905 12 17055950 8.33E-12 6.27E-08
vg1210429306 sf1210426719 12 10429306 1.43E-11 2.78E-06
vg1214847524 sf1214844865 12 14847524 NA 4.36E-08
vg1216278958 sf1216276254 12 16278958 NA 2.45E-07
vg1114869295 sf1114405609 11 14869295 NA 2.48E-06
vg1216724376 sf1216718330 12 16724376 NA 2.51E-06