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 mr1565 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
vg1207040173 sf1207039063 12 7040173 2.22E-20 NA
vg0235056988 sf0235051119 2 35056988 3.67E-18 NA
vg0114119286 sf0114118260 1 14119286 1.24E-17 NA
vg1101821019 sf1101820020 11 1821019 1.93E-17 NA
vg0400372962 sf0400371960 4 372962 3.11E-17 9.30E-07
vg0400373812 sf0400372810 4 373812 4.74E-17 2.82E-07
vg1206313502 sf1206312392 12 6313502 3.11E-16 1.45E-06
vg0401117842 sf0401113392 4 1117842 2.63E-11 2.44E-08
vg1207772422 sf1207769828 12 7772422 NA 7.87E-10
vg0329011730 sf0329004782 3 29011730 NA 1.25E-08
vg0401189541 sf0401185091 4 1189541 NA 1.19E-07
vg0400690170 sf0400689169 4 690170 NA 1.24E-07
vg1227356558 sf1227322958 12 27356558 NA 5.49E-07
vg0434528476 sf0434343369 4 34528476 NA 6.89E-07
vg0400481536 sf0400480534 4 481536 NA 7.67E-07
vg0323951924 sf0323950098 3 23951924 NA 1.53E-06
vg0400913684 sf0400912684 4 913684 NA 1.55E-06
vg0335210290 sf0335203159 3 35210290 NA 1.78E-06