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 mr1925 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
vg0106730666 sf0106729666 1 6730666 5.34E-24 2.41E-24
vg0106731123 sf0106730123 1 6731123 2.84E-23 7.06E-25
vg0106684462 sf0106683462 1 6684462 1.79E-18 1.70E-15
vg0106683798 sf0106682798 1 6683798 2.91E-18 6.47E-16
vg0105640821 sf0105639821 1 5640821 1.78E-15 1.58E-06
vg0130455488 sf0130454444 1 30455488 1.41E-13 NA
vg0330364714 sf0330357753 3 30364714 7.75E-13 NA
vg0106260213 sf0106259213 1 6260213 2.01E-11 7.04E-07
vg1124875808 sf1124409648 11 24875808 2.25E-09 7.27E-09
vg1124954612 sf1124488452 11 24954612 5.25E-09 4.12E-09
vg1125118463 sf1124652303 11 25118463 9.00E-09 3.27E-10
vg1016932373 sf1016861145 10 16932373 1.30E-08 NA
vg1125085953 sf1124619793 11 25085953 2.55E-08 3.61E-09
vg1124972080 sf1124505920 11 24972080 4.02E-08 5.19E-08
vg0106686584 sf0106685584 1 6686584 8.30E-08 2.10E-07
vg0106725146 sf0106724146 1 6725146 9.36E-08 3.57E-06
vg0323946857 sf0323945031 3 23946857 2.84E-07 2.37E-06
vg1107617628 sf1107613373 11 7617628 4.89E-07 NA
vg0624535916 sf0624534919 6 24535916 5.01E-07 2.32E-06
vg1124641235 sf1124175075 11 24641235 8.66E-07 2.97E-07
vg1124898439 sf1124432279 11 24898439 9.95E-07 1.98E-06
vg0105636088 sf0105635088 1 5636088 1.04E-06 4.85E-10
vg0106959659 sf0106958659 1 6959659 NA 1.82E-11
vg0107031364 sf0107030364 1 7031364 NA 7.16E-09
vg0107209160 sf0107208160 1 7209160 NA 3.38E-07
vg0105709551 sf0105708551 1 5709551 NA 4.46E-07
vg0428528974 sf0428343827 4 28528974 NA 5.56E-07
vg1125089512 sf1124623352 11 25089512 NA 1.30E-06