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 mr1408 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
vg0719006525 sf0719005532 7 19006525 4.49E-24 7.79E-19
vg0107214556 sf0107213556 1 7214556 4.29E-13 1.19E-08
vg0408294706 sf0408289980 4 8294706 1.05E-11 3.85E-08
vg0912061274 sf0912060273 9 12061274 9.25E-11 1.86E-07
vg0514963706 sf0514906249 5 14963706 2.26E-10 7.92E-08
vg0700416280 sf0700415280 7 416280 5.30E-10 3.61E-08
vg0419905339 sf0419733375 4 19905339 9.72E-10 2.58E-07
vg0200846970 sf0200846970 2 846970 2.54E-09 7.92E-08
vg0420064379 sf0419892415 4 20064379 3.57E-09 1.76E-06
vg0709019375 sf0709018381 7 9019375 3.97E-09 4.69E-07
vg0309319600 sf0309318536 3 9319600 3.72E-08 2.36E-06
vg0705107520 sf0705106521 7 5107520 5.00E-08 3.78E-06
vg0905696575 sf0905695575 9 5696575 1.02E-07 1.06E-06
vg0124881856 sf0124880812 1 24881856 1.19E-07 2.97E-06
vg0419763927 sf0419591962 4 19763927 5.52E-07 5.34E-08
vg0804028565 sf0804027568 8 4028565 1.77E-06 2.75E-06
vg0719129893 sf0719128900 7 19129893 NA 2.66E-09
vg0828401472 sf0828398758 8 28401472 NA 8.97E-08
vg0419912370 sf0419740406 4 19912370 NA 7.21E-07
vg0413556513 sf0413547227 4 13556513 NA 1.32E-06
vg0721707193 sf0721706200 7 21707193 NA 1.69E-06
vg0422772120 sf0422587003 4 22772120 NA 3.19E-06