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 mr1949 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
vg0719302457 sf0719301464 7 19302457 8.83E-38 1.60E-28
vg0719064221 sf0719063228 7 19064221 1.39E-29 6.88E-33
vg0719057980 sf0719056987 7 19057980 1.44E-19 1.88E-21
vg0719223576 sf0719222583 7 19223576 1.01E-16 7.45E-07
vg0722275425 sf0722274432 7 22275425 1.90E-16 NA
vg0620440814 sf0620439817 6 20440814 3.77E-16 NA
vg0228211032 sf0228205163 2 28211032 5.77E-15 7.66E-06
vg0336362940 sf0336355810 3 36362940 1.48E-14 2.28E-07
vg0336402152 sf0336395022 3 36402152 3.52E-14 1.23E-07
vg0113011816 sf0113010790 1 13011816 2.60E-13 1.43E-08
vg0428494128 sf0428308982 4 28494128 3.36E-13 1.26E-06
vg1103514429 sf1103510332 11 3514429 8.15E-13 2.00E-07
vg0315302142 sf0315300789 3 15302142 1.02E-12 9.19E-07
vg0719055344 sf0719054351 7 19055344 NA 1.72E-21
vg0719198361 sf0719197368 7 19198361 NA 3.24E-16
vg0719449907 sf0719448914 7 19449907 NA 2.11E-11
vg0329561125 sf0329554165 3 29561125 NA 4.14E-09
vg0719436399 sf0719435406 7 19436399 NA 1.03E-08
vg0718961880 sf0718960887 7 18961880 NA 1.41E-08
vg0302581223 sf0302580219 3 2581223 NA 4.48E-08
vg1105544417 sf1105540169 11 5544417 NA 5.83E-08
vg0909775480 sf0909774479 9 9775480 NA 5.91E-08
vg0421592157 sf0421420207 4 21592157 NA 1.69E-07
vg0109818394 sf0109817370 1 9818394 NA 4.10E-07
vg0708134630 sf0708133635 7 8134630 NA 8.22E-07
vg0517797635 sf0517737121 5 17797635 NA 1.04E-06
vg1217503545 sf1217497500 12 17503545 NA 1.51E-06
vg1006706089 sf1006721712 10 6706089 NA 1.60E-06