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 mr1111 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 7.95E-54 7.34E-40
vg0610589825 sf0610588826 6 10589825 1.01E-20 2.45E-21
vg0610460953 sf0610459954 6 10460953 1.53E-18 5.04E-17
vg0611457307 sf0611456308 6 11457307 5.88E-16 7.30E-10
vg0610679932 sf0610678933 6 10679932 6.93E-16 3.85E-20
vg0611322318 sf0611321319 6 11322318 2.31E-14 6.59E-12
vg0920307704 sf0920307223 9 20307704 5.82E-14 NA
vg0611078097 sf0611077098 6 11078097 2.01E-13 1.30E-14
vg0611590585 sf0611589586 6 11590585 2.40E-13 1.92E-12
vg0610609111 sf0610608112 6 10609111 1.02E-12 5.19E-13
vg0610382484 sf0610381485 6 10382484 2.48E-12 2.55E-08
vg0611643367 sf0611642368 6 11643367 3.24E-12 2.00E-14
vg0610556004 sf0610555005 6 10556004 1.40E-11 1.30E-09
vg0610116533 sf0610115534 6 10116533 3.42E-11 2.82E-15
vg0610449310 sf0610448311 6 10449310 4.41E-11 7.03E-11
vg0610613420 sf0610612421 6 10613420 4.75E-11 2.05E-09
vg0617595576 sf0617594579 6 17595576 2.48E-10 3.10E-08
vg0611463000 sf0611462001 6 11463000 3.23E-10 1.02E-08
vg0611562185 sf0611561186 6 11562185 1.40E-09 1.52E-08
vg0610544169 sf0610543170 6 10544169 2.73E-09 5.02E-12
vg0612078079 sf0612077080 6 12078079 1.01E-08 1.23E-08
vg0515926609 sf0515869116 5 15926609 2.57E-08 1.54E-06
vg0618817199 sf0618816202 6 18817199 3.58E-08 8.01E-10
vg0618988041 sf0618987044 6 18988041 3.51E-07 7.96E-11
vg0610873253 sf0610872254 6 10873253 6.55E-07 2.04E-09
vg0613050715 sf0613049716 6 13050715 NA 6.57E-09