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 mr1161 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
vg1007564483 sf1007580095 10 7564483 6.95E-55 1.03E-13
vg0407826844 sf0407822112 4 7826844 2.29E-48 1.78E-07
vg0407825943 sf0407821211 4 7825943 4.74E-47 6.65E-10
vg1010383199 sf1010312020 10 10383199 5.94E-47 NA
vg1202107651 sf1202106649 12 2107651 3.29E-44 5.47E-07
vg1006556408 sf1006572031 10 6556408 4.77E-44 5.07E-14
vg1202107188 sf1202106186 12 2107188 8.28E-44 3.42E-08
vg1009147351 sf1009076212 10 9147351 9.22E-44 7.54E-13
vg0719001075 sf0719000082 7 19001075 1.45E-41 NA
vg0528707182 sf0528644537 5 28707182 5.11E-38 1.47E-07
vg0142683989 sf0142682945 1 42683989 7.03E-33 2.55E-07
vg1008991983 sf1008920844 10 8991983 NA 2.10E-10
vg1006304105 sf1006319728 10 6304105 NA 9.49E-10
vg0222742213 sf0222736344 2 22742213 NA 1.77E-09
vg0407826743 sf0407822011 4 7826743 NA 5.58E-09
vg0710047549 sf0710046555 7 10047549 NA 7.24E-09
vg1009362411 sf1009291232 10 9362411 NA 5.81E-08
vg0403205317 sf0403200920 4 3205317 NA 8.10E-08
vg1006364647 sf1006380270 10 6364647 NA 2.21E-06
vg1010397045 sf1010325866 10 10397045 NA 2.41E-06
vg1006175722 sf1006192264 10 6175722 NA 2.96E-06
vg0222716046 sf0222710177 2 22716046 NA 3.05E-06
vg1008918089 sf1008846950 10 8918089 NA 4.09E-06
vg0110929029 sf0110928005 1 10929029 NA 4.81E-06