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 mr1266 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
vg0818684623 sf0818681910 8 18684623 2.61E-12 2.61E-12
vg0406745243 sf0406740689 4 6745243 2.55E-08 2.55E-08
vg1217863038 sf1217834472 12 17863038 2.91E-08 2.91E-08
vg0825302529 sf0825299815 8 25302529 1.04E-07 1.04E-07
vg1221513464 sf1221480011 12 21513464 1.62E-07 1.62E-07
vg0131565984 sf0131564940 1 31565984 1.76E-07 1.76E-07
vg1101680248 sf1101679249 11 1680248 1.84E-07 1.84E-07
vg0226215115 sf0226209246 2 26215115 2.26E-07 2.26E-07
vg0806090419 sf0806089424 8 6090419 6.25E-07 6.25E-07
vg0700157168 sf0700156168 7 157168 8.90E-07 8.91E-07
vg1211121901 sf1211119265 12 11121901 1.01E-06 1.01E-06
vg0825647950 sf0825645236 8 25647950 1.28E-06 1.28E-06
vg0713426232 sf0713425239 7 13426232 1.51E-06 1.51E-06
vg1216316780 sf1216314076 12 16316780 1.55E-06 1.55E-06
vg0214233942 sf0214228072 2 14233942 1.56E-06 1.56E-06
vg0820031479 sf0820028766 8 20031479 2.01E-06 2.01E-06
vg1124477987 sf1124011827 11 24477987 2.17E-06 2.17E-06
vg0405900244 sf0405895685 4 5900244 2.21E-06 2.21E-06
vg0311038848 sf0311037566 3 11038848 2.40E-06 2.40E-06
vg1006613053 sf1006628676 10 6613053 2.75E-06 2.75E-06