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 mr1227 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
vg0719057980 sf0719056987 7 19057980 1.28E-11 2.78E-07
vg0719407965 sf0719406972 7 19407965 2.07E-11 2.18E-07
vg0405892464 sf0405887905 4 5892464 1.04E-10 1.24E-06
vg0719064944 sf0719063951 7 19064944 3.88E-10 1.09E-07
vg0819137940 sf0819135227 8 19137940 3.98E-10 9.13E-06
vg0514862455 sf0514804998 5 14862455 4.27E-10 NA
vg0218609203 sf0218603334 2 18609203 4.58E-10 4.25E-06
vg0405891709 sf0405887149 4 5891709 1.07E-09 5.90E-07
vg0819149852 sf0819147139 8 19149852 1.68E-09 1.72E-06
vg0809150804 sf0809149808 8 9150804 7.73E-09 NA
vg0208894190 sf0208894188 2 8894190 2.68E-08 NA
vg0816374603 sf0816371889 8 16374603 3.55E-07 6.59E-08
vg1013322658 sf1013251427 10 13322658 4.04E-07 NA
vg0219154244 sf0219148376 2 19154244 5.96E-07 1.78E-06
vg1128595453 sf1128072232 11 28595453 6.00E-07 2.37E-06
vg0124556493 sf0124555449 1 24556493 7.25E-07 NA
vg0719188027 sf0719187034 7 19188027 NA 1.43E-10
vg0327454122 sf0327447175 3 27454122 NA 1.46E-07
vg0818543721 sf0818541008 8 18543721 NA 4.62E-07
vg0305152558 sf0305151560 3 5152558 NA 5.11E-07
vg0428494128 sf0428308982 4 28494128 NA 5.54E-07
vg0805216215 sf0805215218 8 5216215 NA 6.16E-07
vg0402496168 sf0402491768 4 2496168 NA 1.73E-06
vg1215638779 sf1215636076 12 15638779 NA 1.80E-06
vg0305250711 sf0305249711 3 5250711 NA 2.20E-06
vg1125636908 sf1125170747 11 25636908 NA 2.68E-06
vg1010420340 sf1010349161 10 10420340 NA 3.08E-06
vg1017100634 sf1017029406 10 17100634 NA 3.25E-06
vg1017286875 sf1017215648 10 17286875 NA 3.81E-06
vg0906730370 sf0906729370 9 6730370 NA 3.99E-06
vg1212214384 sf1212211722 12 12214384 NA 4.06E-06