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 mr1104 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
vg0719064221 sf0719063228 7 19064221 3.81E-73 4.62E-50
vg0719209499 sf0719208506 7 19209499 6.85E-46 6.49E-12
vg0626833038 sf0626832041 6 26833038 4.69E-44 1.30E-09
vg0708008866 sf0708007871 7 8008866 7.12E-43 2.99E-06
vg0305665264 sf0305664264 3 5665264 5.00E-42 NA
vg0217092847 sf0217086977 2 17092847 5.71E-42 2.83E-07
vg0719055344 sf0719054351 7 19055344 NA 3.61E-35
vg0719091461 sf0719090468 7 19091461 NA 3.74E-34
vg0719065396 sf0719064403 7 19065396 NA 3.30E-30
vg0719192174 sf0719191181 7 19192174 NA 3.10E-24
vg0828401472 sf0828398758 8 28401472 NA 7.51E-18
vg0719436399 sf0719435406 7 19436399 NA 1.43E-14
vg0707667722 sf0707666727 7 7667722 NA 3.19E-14
vg0719466615 sf0719465622 7 19466615 NA 2.00E-12
vg0803630208 sf0803629211 8 3630208 NA 7.17E-12
vg0109818394 sf0109817370 1 9818394 NA 2.52E-11
vg0309319838 sf0309318774 3 9319838 NA 3.26E-11
vg0408294186 sf0408289460 4 8294186 NA 3.29E-11
vg0719618102 sf0719617109 7 19618102 NA 6.55E-11
vg0419832144 sf0419660181 4 19832144 NA 7.82E-11
vg0715275897 sf0715274904 7 15275897 NA 8.53E-11
vg0113087370 sf0113086344 1 13087370 NA 8.68E-11
vg0719452729 sf0719451736 7 19452729 NA 1.24E-10
vg0302581223 sf0302580219 3 2581223 NA 1.34E-10
vg0230189175 sf0230183306 2 30189175 NA 2.37E-10
vg1105544417 sf1105540169 11 5544417 NA 3.01E-10
vg0909775480 sf0909774479 9 9775480 NA 3.56E-10
vg0709019375 sf0709018381 7 9019375 NA 3.62E-10
vg0704482336 sf0704481337 7 4482336 NA 5.67E-10
vg1217507757 sf1217501712 12 17507757 NA 1.13E-09
vg0704902515 sf0704901516 7 4902515 NA 1.21E-09
vg0719049124 sf0719048131 7 19049124 NA 9.67E-07
vg0718999585 sf0718998592 7 18999585 NA 9.90E-07
vg0810833095 sf0810832100 8 10833095 NA 6.20E-06