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 mr1897 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 9.35E-48 2.90E-24
vg0216876411 sf0216870541 2 16876411 1.03E-42 9.20E-26
vg0217519406 sf0217513536 2 17519406 5.75E-40 1.05E-19
vg1220336354 sf1220307796 12 20336354 2.88E-22 1.85E-06
vg0217517982 sf0217512112 2 17517982 4.55E-22 3.56E-11
vg1015182572 sf1015111340 10 15182572 8.89E-21 NA
vg1108225523 sf1108220133 11 8225523 3.00E-19 1.81E-08
vg0723337151 sf0723336158 7 23337151 4.14E-19 NA
vg0217924433 sf0217918564 2 17924433 8.99E-18 2.59E-07
vg0216846900 sf0216841030 2 16846900 1.22E-17 9.29E-11
vg1216728800 sf1216722754 12 16728800 7.40E-17 1.24E-06
vg0217497082 sf0217491212 2 17497082 8.05E-16 7.91E-11
vg0217233564 sf0217227694 2 17233564 1.45E-14 9.92E-07
vg0217029507 sf0217023637 2 17029507 1.53E-13 3.49E-06
vg0212591710 sf0212591706 2 12591710 9.04E-12 4.94E-08
vg0217864346 sf0217858477 2 17864346 8.92E-11 3.87E-06
vg0217163428 sf0217157558 2 17163428 NA 1.36E-18
vg0218543938 sf0218538069 2 18543938 NA 4.14E-11
vg0217494680 sf0217488810 2 17494680 NA 1.44E-09
vg0217025287 sf0217019417 2 17025287 NA 9.21E-09
vg0217221174 sf0217215304 2 17221174 NA 1.77E-07
vg0208695804 sf0208695803 2 8695804 NA 2.01E-07
vg0216600070 sf0216594200 2 16600070 NA 2.26E-07
vg0215745955 sf0215740085 2 15745955 NA 8.51E-07
vg1004572365 sf1004588903 10 4572365 NA 1.37E-06
vg0427400065 sf0427214929 4 27400065 NA 1.97E-06