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 mr1092 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
vg0705313214 sf0705312215 7 5313214 1.02E-50 NA
vg0626572490 sf0626571493 6 26572490 4.28E-50 NA
vg0914708382 sf0914707381 9 14708382 1.06E-49 NA
vg0217547423 sf0217541553 2 17547423 1.68E-49 NA
vg0623734655 sf0623733658 6 23734655 1.99E-49 NA
vg0626494211 sf0626493214 6 26494211 1.55E-47 2.65E-08
vg0118657009 sf0118655963 1 18657009 4.56E-45 3.73E-06
vg1219658723 sf1219630193 12 19658723 1.10E-44 NA
vg0130670983 sf0130669939 1 30670983 NA 9.36E-11
vg0130832570 sf0130831526 1 30832570 NA 1.73E-09
vg0907029568 sf0907028568 9 7029568 NA 8.31E-08
vg0138024269 sf0138023226 1 38024269 NA 1.34E-07
vg0719817684 sf0719816691 7 19817684 NA 2.94E-07
vg0103417535 sf0103416535 1 3417535 NA 3.23E-07
vg0131035257 sf0131034213 1 31035257 NA 3.25E-07
vg1203606223 sf1203605222 12 3606223 NA 5.71E-07
vg0306207246 sf0306206246 3 6207246 NA 5.90E-07
vg0527971405 sf0527908761 5 27971405 NA 1.68E-06
vg0129917132 sf0129916087 1 29917132 NA 1.95E-06
vg0323588254 sf0323586428 3 23588254 NA 2.63E-06
vg1200699466 sf1200698466 12 699466 NA 2.65E-06
vg0628170446 sf0628169448 6 28170446 NA 3.01E-06
vg0717368399 sf0717367406 7 17368399 NA 3.15E-06
vg0420619843 sf0420447886 4 20619843 NA 3.18E-06
vg0102964097 sf0102963097 1 2964097 NA 3.19E-06
vg0129045109 sf0129044064 1 29045109 NA 3.72E-06
vg0907140771 sf0907139771 9 7140771 NA 4.84E-06
vg0322438729 sf0322437218 3 22438729 NA 4.85E-06