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 mr1218 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
vg0610144953 sf0610143954 6 10144953 3.02E-25 3.78E-18
vg0610381116 sf0610380117 6 10381116 2.44E-16 2.22E-10
vg0610362347 sf0610361348 6 10362347 1.21E-15 4.67E-11
vg0617155455 sf0617154458 6 17155455 7.62E-14 1.13E-06
vg0612914787 sf0612913788 6 12914787 1.03E-12 NA
vg0610813941 sf0610812942 6 10813941 4.95E-12 9.04E-09
vg0629121019 sf0629120021 6 29121019 7.15E-11 2.59E-06
vg0611510239 sf0611509240 6 11510239 1.08E-10 1.82E-06
vg0609809561 sf0609808562 6 9809561 2.41E-10 8.74E-07
vg0610444948 sf0610443949 6 10444948 1.03E-09 8.88E-07
vg0610457875 sf0610456876 6 10457875 1.20E-09 2.37E-07
vg0610290318 sf0610289319 6 10290318 1.74E-09 4.62E-06
vg0610375991 sf0610374992 6 10375991 2.55E-09 4.82E-07
vg0606072382 sf0606071383 6 6072382 2.21E-07 4.24E-07
vg0720636944 sf0720635951 7 20636944 1.05E-06 4.65E-08
vg0610071646 sf0610070647 6 10071646 1.77E-06 7.52E-07
vg0721415805 sf0721414812 7 21415805 3.94E-06 4.02E-06
vg0235469783 sf0235463914 2 35469783 NA 4.70E-07
vg0614714911 sf0614713912 6 14714911 NA 1.04E-06
vg0620350630 sf0620349633 6 20350630 NA 1.19E-06
vg1002270223 sf1002269200 10 2270223 NA 1.36E-06
vg0714933670 sf0714932677 7 14933670 NA 3.93E-06
vg0721415417 sf0721414424 7 21415417 NA 4.70E-06