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 mr1728 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
vg0918158744 sf0918157743 9 18158744 3.81E-47 5.95E-22
vg0917595739 sf0917594738 9 17595739 9.69E-32 4.11E-14
vg0916048599 sf0916047598 9 16048599 1.32E-24 5.45E-06
vg0915695679 sf0915694678 9 15695679 1.16E-19 2.35E-06
vg1203687735 sf1203686734 12 3687735 2.43E-16 NA
vg0601966608 sf0601965609 6 1966608 1.61E-15 NA
vg0513549972 sf0513492519 5 13549972 2.05E-15 5.21E-07
vg0433383265 sf0433198154 4 33383265 8.35E-15 4.22E-07
vg0433360330 sf0433175219 4 33360330 4.63E-14 3.48E-06
vg0916208687 sf0916207686 9 16208687 6.17E-13 4.67E-10
vg0919214450 sf0919214040 9 19214450 9.28E-13 3.35E-06
vg0917503526 sf0917502525 9 17503526 NA 5.23E-09
vg0918204237 sf0918203236 9 18204237 NA 1.43E-07
vg0600431653 sf0600430654 6 431653 NA 3.81E-07
vg0800651303 sf0800650303 8 651303 NA 5.40E-07
vg0607378867 sf0607377868 6 7378867 NA 8.20E-07
vg0920504790 sf0920504309 9 20504790 NA 9.90E-07
vg0332159587 sf0332152464 3 32159587 NA 1.26E-06
vg0611005970 sf0611004971 6 11005970 NA 1.40E-06
vg1109811763 sf1109806340 11 9811763 NA 3.26E-06
vg0332124562 sf0332117439 3 32124562 NA 3.33E-06
vg1213724734 sf1213722072 12 13724734 NA 4.70E-06