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 mr1121 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
vg0610566084 sf0610565085 6 10566084 1.58E-49 4.76E-35
vg0610566237 sf0610565238 6 10566237 2.65E-49 1.06E-35
vg0610683043 sf0610682044 6 10683043 1.61E-24 2.70E-19
vg0610444061 sf0610443062 6 10444061 8.53E-17 4.90E-15
vg0610679932 sf0610678933 6 10679932 2.41E-16 7.40E-17
vg0610873460 sf0610872461 6 10873460 5.27E-15 4.30E-11
vg0610584104 sf0610583105 6 10584104 7.33E-15 1.55E-10
vg0610435285 sf0610434286 6 10435285 1.02E-14 3.88E-15
vg0610750291 sf0610749292 6 10750291 3.86E-14 1.22E-10
vg0610116533 sf0610115534 6 10116533 5.46E-14 1.36E-13
vg0610723416 sf0610722417 6 10723416 7.14E-14 3.17E-11
vg0610965158 sf0610964159 6 10965158 4.44E-12 6.93E-10
vg0610556004 sf0610555005 6 10556004 6.38E-11 2.33E-09
vg0615208926 sf0615207927 6 15208926 7.45E-11 7.04E-10
vg0611078097 sf0611077098 6 11078097 1.21E-10 2.36E-11
vg0619254847 sf0619253850 6 19254847 8.45E-10 4.23E-08
vg0609891803 sf0609890804 6 9891803 1.15E-09 1.07E-06
vg0611929029 sf0611928030 6 11929029 3.89E-09 3.17E-07
vg0611643367 sf0611642368 6 11643367 2.52E-08 9.67E-10
vg0613809145 sf0613808146 6 13809145 3.14E-08 5.70E-08
vg0611392640 sf0611391641 6 11392640 4.50E-08 4.13E-07
vg0610611540 sf0610610541 6 10611540 4.93E-08 2.68E-07
vg0816239139 sf0816236425 8 16239139 2.66E-07 1.85E-07
vg0805526977 sf0805525980 8 5526977 3.07E-07 6.90E-08
vg0619171840 sf0619170843 6 19171840 3.34E-07 6.48E-10
vg1213234449 sf1213231787 12 13234449 NA 7.49E-07
vg0401225967 sf0401221517 4 1225967 NA 7.90E-07