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 mr1085 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
vg0719064331 sf0719063338 7 19064331 1.67E-54 7.96E-29
vg0626879116 sf0626878119 6 26879116 9.23E-40 2.49E-09
vg0304917111 sf0304916113 3 4917111 1.60E-38 6.82E-07
vg1017940888 sf1017869660 10 17940888 3.92E-38 1.62E-06
vg0706502696 sf0706501701 7 6502696 1.08E-37 8.13E-07
vg0706507299 sf0706506304 7 6507299 6.49E-37 6.74E-07
vg0719091461 sf0719090468 7 19091461 NA 7.74E-18
vg0719055344 sf0719054351 7 19055344 NA 8.32E-17
vg0719045166 sf0719044173 7 19045166 NA 6.89E-12
vg0719141601 sf0719140608 7 19141601 NA 3.00E-11
vg0719145627 sf0719144634 7 19145627 NA 4.05E-11
vg0719466615 sf0719465622 7 19466615 NA 1.29E-10
vg0828401472 sf0828398758 8 28401472 NA 2.38E-10
vg0719065396 sf0719064403 7 19065396 NA 3.90E-10
vg0707076224 sf0707075229 7 7076224 NA 1.19E-09
vg0719452729 sf0719451736 7 19452729 NA 6.12E-09
vg0113087370 sf0113086344 1 13087370 NA 7.79E-09
vg0919718025 sf0919717615 9 19718025 NA 4.87E-08
vg0619424530 sf0619423533 6 19424530 NA 6.37E-08
vg0230189175 sf0230183306 2 30189175 NA 8.51E-08
vg0719527870 sf0719526877 7 19527870 NA 1.43E-07
vg0719436399 sf0719435406 7 19436399 NA 1.44E-07
vg0616985717 sf0616984720 6 16985717 NA 1.58E-07
vg0434575713 sf0434390605 4 34575713 NA 1.71E-07
vg1217302382 sf1217296337 12 17302382 NA 1.82E-07
vg0616954672 sf0616953675 6 16954672 NA 1.87E-07
vg0315333320 sf0315331967 3 15333320 NA 1.99E-07
vg0707063094 sf0707062099 7 7063094 NA 4.88E-07
vg1217507757 sf1217501712 12 17507757 NA 5.94E-07
vg0810149802 sf0810148806 8 10149802 NA 2.40E-06