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 mr1745 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
vg1125263550 sf1124797390 11 25263550 1.63E-16 8.13E-07
vg1125125737 sf1124659577 11 25125737 7.25E-13 2.42E-07
vg0432437759 sf0432252650 4 32437759 1.94E-11 NA
vg1214757149 sf1214754490 12 14757149 1.95E-09 NA
vg1114596184 sf1114132502 11 14596184 2.48E-09 NA
vg0507714473 sf0507714414 5 7714473 6.60E-09 NA
vg1226938080 sf1226904479 12 26938080 2.15E-08 3.74E-06
vg0427745854 sf0427560717 4 27745854 9.46E-08 2.67E-06
vg1109530315 sf1109524892 11 9530315 5.43E-07 1.42E-06
vg0402221936 sf0402217531 4 2221936 7.63E-07 NA
vg0718871778 sf0718870785 7 18871778 9.06E-06 NA
vg0107150999 sf0107149999 1 7150999 NA 3.16E-06
vg0714435991 sf0714434998 7 14435991 NA 8.45E-06