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 mr1103 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
vg0719135307 sf0719134314 7 19135307 3.61E-79 2.01E-29
vg0719049906 sf0719048913 7 19049906 1.26E-78 5.49E-35
vg0719001862 sf0719000869 7 19001862 9.23E-74 6.52E-18
vg0917918788 sf0917917787 9 17918788 1.02E-66 NA
vg0620879823 sf0620878826 6 20879823 1.18E-64 NA
vg0708204553 sf0708203558 7 8204553 2.61E-63 9.05E-06
vg0704138775 sf0704137776 7 4138775 5.06E-62 NA
vg0220550093 sf0220544225 2 20550093 6.60E-61 5.44E-06
vg0620448711 sf0620447714 6 20448711 1.09E-57 5.01E-07
vg0719091461 sf0719090468 7 19091461 NA 3.44E-29
vg0719055344 sf0719054351 7 19055344 NA 2.81E-21
vg0719345198 sf0719344205 7 19345198 NA 9.41E-13
vg0719466615 sf0719465622 7 19466615 NA 5.38E-12
vg0719030291 sf0719029298 7 19030291 NA 6.68E-10
vg0421592157 sf0421420207 4 21592157 NA 1.75E-09
vg0329561125 sf0329554165 3 29561125 NA 2.60E-09
vg0909775480 sf0909774479 9 9775480 NA 8.08E-09
vg0720529894 sf0720528901 7 20529894 NA 1.30E-08
vg0718999754 sf0718998761 7 18999754 NA 1.35E-08
vg0718955684 sf0718954691 7 18955684 NA 2.65E-08
vg0719067465 sf0719066472 7 19067465 NA 4.59E-08
vg1105544417 sf1105540169 11 5544417 NA 4.61E-08
vg0136510873 sf0136509830 1 36510873 NA 7.68E-08
vg0708134630 sf0708133635 7 8134630 NA 9.37E-08
vg0428494128 sf0428308982 4 28494128 NA 1.85E-07
vg0620149548 sf0620148551 6 20149548 NA 5.99E-07
vg0122988831 sf0122987787 1 22988831 NA 6.12E-07
vg0620744993 sf0620743996 6 20744993 NA 6.48E-07
vg0104223122 sf0104222122 1 4223122 NA 6.85E-07
vg1120455169 sf1119989094 11 20455169 NA 7.98E-07