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 mr1486 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
vg1001305839 sf1001304816 10 1305839 7.95E-21 9.28E-25
vg1001271744 sf1001270721 10 1271744 4.40E-18 6.85E-21
vg1001244211 sf1001243188 10 1244211 1.73E-17 1.17E-12
vg1001227179 sf1001226156 10 1227179 6.68E-16 4.35E-19
vg1001229450 sf1001228427 10 1229450 6.94E-16 2.43E-19
vg1001274276 sf1001273253 10 1274276 4.09E-15 7.84E-16
vg1001446001 sf1001444978 10 1446001 1.25E-14 5.87E-12
vg1001527825 sf1001526802 10 1527825 2.63E-14 8.51E-13
vg0720058754 sf0720057761 7 20058754 6.44E-13 2.63E-08
vg0720057093 sf0720056100 7 20057093 1.39E-12 1.54E-08
vg1001306734 sf1001305711 10 1306734 3.82E-12 3.13E-11
vg0507685756 sf0507685697 5 7685756 5.61E-09 6.67E-08
vg1001243731 sf1001242708 10 1243731 6.93E-09 2.27E-10
vg0715967548 sf0715966555 7 15967548 3.75E-08 3.02E-07
vg0410187931 sf0410178628 4 10187931 1.62E-07 8.81E-07
vg0412555488 sf0412546198 4 12555488 1.85E-07 8.88E-07
vg1001434429 sf1001433406 10 1434429 7.54E-07 3.57E-09
vg0818608910 sf0818606197 8 18608910 1.74E-06 6.29E-08
vg0216592863 sf0216586993 2 16592863 2.00E-06 NA
vg0922086583 sf0922086102 9 22086583 3.90E-06 1.19E-06
vg1002107770 sf1002106747 10 2107770 6.34E-06 2.59E-09
vg0420863715 sf0420691758 4 20863715 NA 4.65E-07
vg1203735229 sf1203734228 12 3735229 NA 7.70E-07
vg1022763526 sf1022691999 10 22763526 NA 1.63E-06
vg1001287549 sf1001286526 10 1287549 NA 1.81E-06
vg1001790681 sf1001789658 10 1790681 NA 1.82E-06