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 mr1115 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
vg0604494709 sf0604493710 6 4494709 7.30E-39 2.04E-12
vg0604342875 sf0604341876 6 4342875 2.06E-37 1.26E-13
vg0604336777 sf0604335778 6 4336777 1.39E-36 2.85E-15
vg0805128532 sf0805127535 8 5128532 4.34E-32 NA
vg0140038034 sf0140036991 1 40038034 7.89E-32 NA
vg0811152944 sf0811151949 8 11152944 2.35E-31 1.84E-06
vg1117795643 sf1117329499 11 17795643 7.55E-31 NA
vg0428886321 sf0428701178 4 28886321 8.48E-30 3.82E-06
vg0604359243 sf0604358244 6 4359243 NA 1.02E-09
vg0402111447 sf0402107041 4 2111447 NA 3.82E-08
vg1004059501 sf1004058477 10 4059501 NA 1.24E-06
vg0604369775 sf0604368776 6 4369775 NA 1.45E-06
vg0317363099 sf0317361909 3 17363099 NA 1.48E-06
vg0604526918 sf0604525919 6 4526918 NA 1.63E-06
vg0431387810 sf0431202708 4 31387810 NA 2.63E-06
vg1207388082 sf1207385489 12 7388082 NA 2.86E-06
vg0432523363 sf0432338255 4 32523363 NA 2.92E-06
vg0804049852 sf0804048855 8 4049852 NA 2.92E-06
vg1219133094 sf1219104530 12 19133094 NA 3.57E-06
vg0603039595 sf0603038596 6 3039595 NA 3.74E-06
vg0140085612 sf0140084569 1 40085612 NA 3.80E-06
vg0518984986 sf0518922470 5 18984986 NA 4.24E-06
vg0207745647 sf0207745646 2 7745647 NA 4.93E-06
vg1214782030 sf1214779371 12 14782030 NA 7.99E-06