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 mr1117 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
vg0222679274 sf0222673405 2 22679274 5.79E-52 1.39E-23
vg0222675535 sf0222669666 2 22675535 3.80E-50 3.93E-25
vg0222739148 sf0222733279 2 22739148 3.92E-39 1.72E-20
vg0110304750 sf0110303726 1 10304750 4.05E-29 4.37E-07
vg0526722696 sf0526660054 5 26722696 8.62E-29 9.33E-07
vg1110783636 sf1110778181 11 10783636 2.07E-28 1.19E-08
vg0518201525 sf0518141011 5 18201525 2.94E-28 1.62E-07
vg1110740880 sf1110735425 11 10740880 3.35E-27 2.21E-09
vg0505887711 sf0505887649 5 5887711 5.86E-27 1.77E-07
vg0518620627 sf0518558110 5 18620627 1.53E-26 1.26E-07
vg0500664660 sf0500664660 5 664660 3.63E-26 2.66E-10
vg0818212763 sf0818210050 8 18212763 4.33E-26 1.12E-08
vg0306047262 sf0306046262 3 6047262 7.35E-26 4.03E-08
vg0221507264 sf0221501395 2 21507264 4.43E-21 3.29E-06
vg0222952563 sf0222946694 2 22952563 1.64E-19 2.01E-13
vg1117961699 sf1117495557 11 17961699 4.35E-18 1.27E-07
vg0315922266 sf0315920913 3 15922266 4.53E-18 9.86E-07
vg0222722554 sf0222716685 2 22722554 NA 2.41E-09
vg1204507349 sf1204506337 12 4507349 NA 4.15E-09
vg0709837399 sf0709836405 7 9837399 NA 4.71E-09
vg0140888130 sf0140887087 1 40888130 NA 9.46E-09
vg1209218924 sf1209216333 12 9218924 NA 1.30E-08
vg0822600721 sf0822598008 8 22600721 NA 1.96E-08
vg0327037726 sf0327030779 3 27037726 NA 2.14E-08
vg0315713125 sf0315711772 3 15713125 NA 5.15E-08
vg0401716915 sf0401712464 4 1716915 NA 6.36E-08
vg1021149005 sf1021077484 10 21149005 NA 7.80E-08
vg0224791200 sf0224785331 2 24791200 NA 8.03E-08
vg0222271516 sf0222265647 2 22271516 NA 8.80E-08
vg1005950387 sf1005966925 10 5950387 NA 8.95E-08
vg0819585965 sf0819583252 8 19585965 NA 1.09E-07
vg0626215270 sf0626214273 6 26215270 NA 1.40E-07
vg0139710848 sf0139709805 1 39710848 NA 1.51E-07
vg0421275808 sf0421103862 4 21275808 NA 1.84E-07
vg0303832565 sf0303831561 3 3832565 NA 1.02E-06
vg0333133374 sf0333126244 3 33133374 NA 7.61E-06