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 mr1143 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 4.63E-24 NA
vg0701923849 sf0701922850 7 1923849 5.17E-23 NA
vg0133244648 sf0133243604 1 33244648 2.57E-21 NA
vg1217046946 sf1217040900 12 17046946 3.70E-21 NA
vg0329606120 sf0329599160 3 29606120 3.93E-21 NA
vg0405865352 sf0405860793 4 5865352 7.80E-18 3.20E-06
vg0420896565 sf0420724609 4 20896565 8.65E-17 NA
vg1020708879 sf1020637358 10 20708879 1.03E-16 5.99E-07
vg0803262517 sf0803261520 8 3262517 NA 3.79E-07
vg0520332453 sf0520269926 5 20332453 NA 1.26E-06
vg0420830218 sf0420658261 4 20830218 NA 1.78E-06
vg1003735001 sf1003733978 10 3735001 NA 3.08E-06
vg0128866911 sf0128865866 1 28866911 NA 4.73E-06
vg0414518378 sf0414509092 4 14518378 NA 6.42E-06