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 mr1167 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
vg0404341374 sf0404336979 4 4341374 7.12E-24 NA
vg0701923849 sf0701922850 7 1923849 1.89E-23 NA
vg1217066010 sf1217059965 12 17066010 1.78E-22 NA
vg0113904382 sf0113903356 1 13904382 2.23E-21 NA
vg0140491926 sf0140490883 1 40491926 5.48E-21 NA
vg0620234044 sf0620233047 6 20234044 1.40E-17 4.73E-06
vg0620203384 sf0620202387 6 20203384 5.41E-17 6.92E-06
vg1020708879 sf1020637358 10 20708879 8.68E-17 1.05E-06
vg0405876106 sf0405871547 4 5876106 1.29E-15 7.86E-06
vg1003735001 sf1003733978 10 3735001 NA 4.05E-07
vg0420830218 sf0420658261 4 20830218 NA 7.98E-07
vg0803262517 sf0803261520 8 3262517 NA 2.22E-06
vg0430611290 sf0430426165 4 30611290 NA 3.20E-06