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 mr1927 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
vg0217114921 sf0217109051 2 17114921 2.62E-61 4.27E-31
vg0217071746 sf0217065876 2 17071746 3.10E-61 7.01E-32
vg0217095683 sf0217089813 2 17095683 6.22E-61 6.25E-32
vg0217125856 sf0217119986 2 17125856 1.54E-36 2.56E-24
vg0217162430 sf0217156560 2 17162430 4.12E-36 1.53E-24
vg1220336354 sf1220307796 12 20336354 9.63E-29 1.22E-07
vg1015182556 sf1015111324 10 15182556 1.12E-27 NA
vg0723337151 sf0723336158 7 23337151 3.74E-23 NA
vg0217940995 sf0217935126 2 17940995 2.85E-22 1.74E-12
vg1108225523 sf1108220133 11 8225523 4.19E-20 1.64E-08
vg0217861925 sf0217856056 2 17861925 2.17E-19 3.79E-08
vg0121235022 sf0121233977 1 21235022 2.77E-19 NA
vg0217474288 sf0217468418 2 17474288 1.14E-16 1.14E-13
vg0217497082 sf0217491212 2 17497082 NA 8.29E-10
vg0217540070 sf0217534200 2 17540070 NA 1.01E-09
vg0217027791 sf0217021921 2 17027791 NA 4.99E-08
vg0217025287 sf0217019417 2 17025287 NA 1.97E-07
vg0218547738 sf0218541869 2 18547738 NA 3.16E-07
vg1216728542 sf1216722496 12 16728542 NA 5.85E-07
vg1005364864 sf1005381401 10 5364864 NA 1.90E-06
vg1005364284 sf1005380821 10 5364284 NA 3.92E-06
vg0422159758 sf0421974639 4 22159758 NA 4.14E-06