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 mr1676 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
vg0919860310 sf0919859829 9 19860310 4.66E-19 2.17E-10
vg0920140858 sf0920140377 9 20140858 8.32E-18 3.92E-13
vg0920147018 sf0920146537 9 20147018 8.60E-18 4.18E-13
vg0305233552 sf0305232552 3 5233552 1.66E-11 5.00E-07
vg0920177833 sf0920177352 9 20177833 6.14E-11 1.84E-06
vg0918171292 sf0918170291 9 18171292 4.85E-10 9.29E-07
vg0501096643 sf0501096627 5 1096643 7.81E-10 9.19E-06
vg0107015621 sf0107014621 1 7015621 2.61E-09 5.27E-07
vg1210599267 sf1210596680 12 10599267 3.05E-09 2.98E-07
vg0216865447 sf0216859577 2 16865447 1.24E-08 2.46E-06
vg1215651375 sf1215648672 12 15651375 1.27E-08 2.68E-06
vg0400894219 sf0400893219 4 894219 1.46E-08 3.29E-06
vg0137602014 sf0137600971 1 37602014 1.73E-07 1.19E-06
vg0128990759 sf0128989714 1 28990759 3.07E-07 3.15E-06
vg0809383292 sf0809382296 8 9383292 5.35E-07 1.40E-06
vg1017312673 sf1017241446 10 17312673 6.88E-06 NA
vg1005421909 sf1005438446 10 5421909 NA 2.66E-06