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
vg1215966147 sf1215963443 12 15966147 1.94E-70 1.26E-38
vg1215955784 sf1215953080 12 15955784 1.94E-70 1.26E-38
vg0500829493 sf0500829475 5 829493 5.83E-22 NA
vg1212873997 sf1212871336 12 12873997 5.08E-21 3.83E-07
vg1011512136 sf1011440955 10 11512136 4.78E-20 1.39E-07
vg0805528297 sf0805527300 8 5528297 5.91E-20 NA
vg1212876560 sf1212873899 12 12876560 9.29E-19 1.05E-08
vg1209431333 sf1209428742 12 9431333 1.32E-17 6.03E-08
vg1212065475 sf1212062811 12 12065475 1.32E-17 6.03E-08
vg1204609935 sf1204608923 12 4609935 1.71E-16 2.91E-08
vg0810425666 sf0810424670 8 10425666 4.21E-15 3.08E-07
vg1218663003 sf1218634438 12 18663003 1.12E-14 1.98E-11
vg1202777536 sf1202776538 12 2777536 1.70E-14 2.06E-07
vg0919139277 sf0919138866 9 19139277 3.26E-14 5.55E-08
vg1006587700 sf1006603323 10 6587700 1.27E-13 1.89E-10
vg1215852700 sf1215849996 12 15852700 NA 2.54E-16
vg1022588644 sf1022517118 10 22588644 NA 7.07E-11
vg1213186520 sf1213183858 12 13186520 NA 1.04E-08
vg0901555680 sf0901554680 9 1555680 NA 1.10E-08
vg0408293903 sf0408289177 4 8293903 NA 1.25E-08
vg1011512046 sf1011440865 10 11512046 NA 1.93E-08
vg1211633613 sf1211630949 12 11633613 NA 7.66E-08
vg0623791757 sf0623790760 6 23791757 NA 2.14E-07
vg0318783105 sf0318781865 3 18783105 NA 3.93E-07
vg0715496678 sf0715495685 7 15496678 NA 6.07E-07
vg1212876949 sf1212874288 12 12876949 NA 6.67E-07