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 mr1226 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
vg0719049906 sf0719048913 7 19049906 1.15E-64 3.79E-57
vg0917918788 sf0917917787 9 17918788 1.65E-45 NA
vg1017974478 sf1017903250 10 17974478 5.53E-45 NA
vg0215980294 sf0215974424 2 15980294 6.78E-45 NA
vg1101084691 sf1101083692 11 1084691 1.10E-44 NA
vg0917985172 sf0917984171 9 17985172 8.07E-40 NA
vg0719055344 sf0719054351 7 19055344 NA 1.08E-44
vg0719141601 sf0719140608 7 19141601 NA 8.98E-31
vg0719091461 sf0719090468 7 19091461 NA 9.19E-31
vg0719067465 sf0719066472 7 19067465 NA 1.75E-28
vg0719141573 sf0719140580 7 19141573 NA 4.57E-22
vg0828401472 sf0828398758 8 28401472 NA 3.77E-16
vg0719436399 sf0719435406 7 19436399 NA 5.56E-15
vg0719466615 sf0719465622 7 19466615 NA 5.96E-15
vg0707667722 sf0707666727 7 7667722 NA 1.02E-14
vg0329561125 sf0329554165 3 29561125 NA 2.75E-13
vg0408294186 sf0408289460 4 8294186 NA 1.32E-12
vg1105544417 sf1105540169 11 5544417 NA 3.82E-12
vg0327720515 sf0327713568 3 27720515 NA 5.11E-12
vg0719040975 sf0719039982 7 19040975 NA 9.55E-12
vg0302581223 sf0302580219 3 2581223 NA 1.60E-11
vg0109818394 sf0109817370 1 9818394 NA 6.50E-11
vg1217302382 sf1217296337 12 17302382 NA 1.67E-10
vg1217507757 sf1217501712 12 17507757 NA 1.68E-10
vg0421592157 sf0421420207 4 21592157 NA 1.72E-10
vg0617336375 sf0617335378 6 17336375 NA 1.72E-10
vg0719618102 sf0719617109 7 19618102 NA 1.77E-10
vg0107216421 sf0107215421 1 7216421 NA 2.20E-10
vg0719060385 sf0719059392 7 19060385 NA 2.41E-10
vg0130136705 sf0130135660 1 30136705 NA 2.59E-10
vg1216808328 sf1216802282 12 16808328 NA 2.85E-10
vg0422489098 sf0422303985 4 22489098 NA 2.87E-10
vg0419906517 sf0419734553 4 19906517 NA 7.65E-10
vg0719090547 sf0719089554 7 19090547 NA 3.91E-06