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 mr1835 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
vg1102070220 sf1102066078 11 2070220 3.02E-12 3.46E-08
vg0405918527 sf0405913968 4 5918527 2.68E-09 NA
vg0224205447 sf0224199578 2 24205447 1.35E-08 7.65E-06
vg0410390630 sf0410381329 4 10390630 2.16E-08 NA
vg0225146033 sf0225140164 2 25146033 2.67E-08 4.12E-06
vg0200630803 sf0200630803 2 630803 4.30E-08 NA
vg0710985476 sf0710984482 7 10985476 9.90E-08 1.25E-06
vg0722555376 sf0722554383 7 22555376 2.51E-07 4.99E-06
vg0409805289 sf0409795987 4 9805289 6.65E-07 9.70E-07
vg1207511374 sf1207508780 12 7511374 2.43E-06 4.71E-06
vg1109631523 sf1109626100 11 9631523 5.22E-06 NA
vg1219079385 sf1219050821 12 19079385 9.84E-06 7.87E-07