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 mr1624 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
vg0710326904 sf0710325910 7 10326904 9.75E-14 NA
vg1002292435 sf1002291412 10 2292435 3.62E-13 2.32E-06
vg1002291312 sf1002290289 10 2291312 3.65E-13 1.39E-06
vg0713088295 sf0713087302 7 13088295 3.90E-13 NA
vg1000306951 sf1000305951 10 306951 4.12E-13 NA
vg1218067516 sf1218038952 12 18067516 3.01E-12 3.66E-06
vg1000147807 sf1000146807 10 147807 4.54E-12 1.14E-06
vg1009983410 sf1009912231 10 9983410 1.12E-10 1.35E-06
vg1210604872 sf1210602285 12 10604872 1.24E-10 NA
vg1011081452 sf1011010272 10 11081452 8.16E-10 NA
vg0816082154 sf0816079440 8 16082154 4.99E-09 3.06E-06
vg1022686258 sf1022614732 10 22686258 1.21E-08 1.78E-06
vg0805117375 sf0805116378 8 5117375 1.30E-08 2.67E-06
vg0719018483 sf0719017490 7 19018483 3.66E-08 NA
vg1100795910 sf1100794911 11 795910 NA 4.80E-06