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 mr1234 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
vg0610564701 sf0610563702 6 10564701 1.13E-99 1.72E-26
vg0610459123 sf0610458124 6 10459123 5.15E-90 4.32E-28
vg0610585146 sf0610584147 6 10585146 1.71E-78 5.14E-19
vg0719240469 sf0719239476 7 19240469 9.59E-61 NA
vg0616950705 sf0616949708 6 16950705 4.92E-59 7.84E-06
vg0122402967 sf0122401922 1 22402967 4.35E-56 NA
vg0617319066 sf0617318069 6 17319066 2.33E-55 4.51E-09
vg0708747195 sf0708746200 7 8747195 1.21E-52 NA
vg0612996928 sf0612995929 6 12996928 1.95E-52 3.41E-08
vg0909341959 sf0909340958 9 9341959 1.00E-45 NA
vg0610788671 sf0610787672 6 10788671 NA 4.55E-13
vg0609920649 sf0609919650 6 9920649 NA 2.19E-12
vg0611723713 sf0611722714 6 11723713 NA 7.08E-10
vg0610787629 sf0610786630 6 10787629 NA 1.33E-08
vg0610779574 sf0610778575 6 10779574 NA 2.22E-08
vg0611888139 sf0611887140 6 11888139 NA 3.26E-08
vg0610676484 sf0610675485 6 10676484 NA 4.87E-08
vg0609649171 sf0609648172 6 9649171 NA 8.81E-08
vg0614543893 sf0614542894 6 14543893 NA 1.76E-07
vg0611561231 sf0611560232 6 11561231 NA 2.05E-07
vg0610360687 sf0610359688 6 10360687 NA 2.13E-07
vg0610061410 sf0610060411 6 10061410 NA 2.36E-07
vg0610143043 sf0610142044 6 10143043 NA 4.48E-07
vg0610587682 sf0610586683 6 10587682 NA 6.13E-07
vg0614107939 sf0614106940 6 14107939 NA 7.55E-07
vg0623041409 sf0623040412 6 23041409 NA 9.88E-07
vg0804365144 sf0804364147 8 4365144 NA 1.04E-06
vg0617636590 sf0617635593 6 17636590 NA 1.08E-06
vg1127696861 sf1127225248 11 27696861 NA 1.23E-06
vg0616129303 sf0616128305 6 16129303 NA 3.94E-06