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
vg1215966147 sf1215963443 12 15966147 1.10E-74 9.22E-41
vg1215955784 sf1215953080 12 15955784 1.10E-74 9.22E-41
vg0500829493 sf0500829475 5 829493 2.38E-22 NA
vg1212873997 sf1212871336 12 12873997 5.59E-21 1.42E-06
vg0805528297 sf0805527300 8 5528297 7.28E-21 2.00E-06
vg1011512136 sf1011440955 10 11512136 2.26E-20 1.58E-07
vg1212876560 sf1212873899 12 12876560 1.44E-18 1.64E-08
vg0810425666 sf0810424670 8 10425666 1.34E-15 1.38E-07
vg1218663003 sf1218634438 12 18663003 3.65E-15 3.27E-12
vg1006587700 sf1006603323 10 6587700 1.21E-14 5.74E-12
vg0919139277 sf0919138866 9 19139277 5.47E-14 1.30E-07
vg1215852700 sf1215849996 12 15852700 NA 1.01E-16
vg1022588644 sf1022517118 10 22588644 NA 2.62E-12
vg0901555680 sf0901554680 9 1555680 NA 1.57E-09
vg0408293903 sf0408289177 4 8293903 NA 6.50E-09
vg1211633613 sf1211630949 12 11633613 NA 9.02E-09
vg1213186520 sf1213183858 12 13186520 NA 1.01E-08
vg1011512046 sf1011440865 10 11512046 NA 1.79E-08
vg1208048502 sf1208045908 12 8048502 NA 1.18E-07
vg0623791757 sf0623790760 6 23791757 NA 1.62E-07
vg0715496678 sf0715495685 7 15496678 NA 2.09E-07
vg1212876949 sf1212874288 12 12876949 NA 2.72E-07
vg0717043053 sf0717042060 7 17043053 NA 3.83E-07
vg0318783105 sf0318781865 3 18783105 NA 4.62E-07
vg0820168380 sf0820165667 8 20168380 NA 5.14E-07
vg0809152994 sf0809151998 8 9152994 NA 5.79E-07
vg1216585567 sf1216582860 12 16585567 NA 6.98E-07