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 mr1072 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
vg0222742146 sf0222736277 2 22742146 9.32E-59 7.37E-39
vg0222739831 sf0222733962 2 22739831 1.35E-58 1.56E-39
vg0223663746 sf0223657877 2 23663746 1.27E-17 4.39E-12
vg0224477817 sf0224471948 2 24477817 9.07E-15 1.04E-07
vg1112606104 sf1112142307 11 12606104 4.55E-14 4.36E-07
vg0224832365 sf0224826496 2 24832365 7.31E-14 7.28E-08
vg0223556553 sf0223550684 2 23556553 1.31E-13 6.61E-07
vg0224640486 sf0224634617 2 24640486 3.13E-13 2.22E-06
vg0224382271 sf0224376402 2 24382271 9.56E-13 6.58E-09
vg0222765370 sf0222759501 2 22765370 8.28E-11 1.14E-06
vg0223903508 sf0223897639 2 23903508 1.68E-10 9.45E-07
vg0225400091 sf0225394222 2 25400091 2.04E-10 2.33E-07
vg0222672664 sf0222666795 2 22672664 1.15E-09 1.40E-10
vg0626053134 sf0626052137 6 26053134 3.58E-09 3.75E-06
vg0222664546 sf0222658677 2 22664546 6.08E-09 1.28E-06
vg0226041405 sf0226035536 2 26041405 9.07E-09 2.12E-06
vg0119711427 sf0119710382 1 19711427 1.51E-08 NA
vg0223048890 sf0223043021 2 23048890 1.58E-07 1.98E-06
vg0610674563 sf0610673564 6 10674563 NA 1.54E-06
vg0225413749 sf0225407880 2 25413749 NA 2.99E-06
vg0107829155 sf0107828155 1 7829155 NA 4.03E-06