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 mr1807 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
vg0129975464 sf0129974419 1 29975464 6.81E-25 NA
vg0520472420 sf0520409891 5 20472420 6.84E-24 NA
vg0507129275 sf0507129217 5 7129275 1.98E-23 3.78E-09
vg1005861727 sf1005878265 10 5861727 1.11E-22 NA
vg1008772538 sf1008701400 10 8772538 1.47E-22 NA
vg0624084602 sf0624083605 6 24084602 3.32E-18 NA
vg0304724456 sf0304723458 3 4724456 3.70E-15 3.03E-07
vg0507128411 sf0507128353 5 7128411 5.80E-14 1.53E-10
vg0507210481 sf0507210423 5 7210481 NA 6.48E-08
vg1119892699 sf1119426622 11 19892699 NA 1.57E-07
vg1125033475 sf1124567315 11 25033475 NA 7.86E-07
vg1120079549 sf1119613472 11 20079549 NA 1.22E-06
vg0419536798 sf0419364836 4 19536798 NA 1.32E-06
vg1100919003 sf1100918004 11 919003 NA 1.55E-06
vg0720910687 sf0720909694 7 20910687 NA 1.62E-06
vg0719933733 sf0719932740 7 19933733 NA 2.30E-06
vg0824240876 sf0824238162 8 24240876 NA 3.67E-06
vg0500026688 sf0500026688 5 26688 NA 9.32E-06