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 mr1613 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
vg0406519287 sf0406514730 4 6519287 5.44E-40 2.95E-31
vg0406562314 sf0406557757 4 6562314 1.73E-35 4.98E-25
vg1122924753 sf1122458624 11 22924753 1.56E-13 1.21E-09
vg0228539625 sf0228533756 2 28539625 6.91E-12 8.32E-09
vg0807117547 sf0807116552 8 7117547 9.31E-12 3.39E-09
vg1122613532 sf1122147403 11 22613532 2.48E-11 2.31E-08
vg1123064026 sf1122597897 11 23064026 6.65E-11 8.43E-09
vg1209921454 sf1209918864 12 9921454 1.34E-09 1.01E-09
vg0406056747 sf0406052186 4 6056747 1.94E-09 6.22E-07
vg1222295817 sf1222262364 12 22295817 2.06E-08 8.48E-07
vg0801674326 sf0801673328 8 1674326 3.23E-08 2.75E-07
vg1003486707 sf1003485684 10 3486707 5.41E-08 1.16E-06
vg0202518756 sf0202518754 2 2518756 2.11E-07 2.40E-07
vg0333972137 sf0333965007 3 33972137 2.43E-07 1.04E-06
vg0430673937 sf0430488812 4 30673937 3.66E-07 1.63E-07
vg0614107939 sf0614106940 6 14107939 1.89E-06 4.50E-09
vg1206256269 sf1206255159 12 6256269 8.57E-06 5.60E-07
vg0233608236 sf0233602367 2 33608236 NA 8.97E-08
vg0114364662 sf0114363636 1 14364662 NA 6.40E-07
vg1128773900 sf1128250679 11 28773900 NA 8.02E-07
vg1100371980 sf1100370982 11 371980 NA 9.19E-07