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 mr1124 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
vg0222741535 sf0222735666 2 22741535 6.31E-118 1.25E-49
vg0222747179 sf0222741310 2 22747179 7.44E-118 7.64E-50
vg0626823010 sf0626822013 6 26823010 6.45E-67 NA
vg0705549250 sf0705548251 7 5549250 6.87E-65 NA
vg0623231357 sf0623230360 6 23231357 7.30E-61 NA
vg0114584013 sf0114582987 1 14584013 7.01E-60 NA
vg0222725003 sf0222719134 2 22725003 NA 3.19E-19
vg0610592581 sf0610591582 6 10592581 NA 8.52E-11
vg0222857256 sf0222851387 2 22857256 NA 3.88E-09
vg0222817468 sf0222811599 2 22817468 NA 1.25E-08
vg0223769163 sf0223763294 2 23769163 NA 1.34E-08
vg0224509150 sf0224503281 2 24509150 NA 1.15E-07
vg0225999747 sf0225993878 2 25999747 NA 4.12E-07
vg0922295660 sf0922295179 9 22295660 NA 4.76E-07
vg0610114266 sf0610113267 6 10114266 NA 1.25E-06
vg0129623819 sf0129622774 1 29623819 NA 1.37E-06
vg0429377757 sf0429192623 4 29377757 NA 1.80E-06
vg0129598466 sf0129597421 1 29598466 NA 1.82E-06
vg0610917532 sf0610916533 6 10917532 NA 2.07E-06
vg1120088079 sf1119622002 11 20088079 NA 2.20E-06
vg0222778319 sf0222772450 2 22778319 NA 2.32E-06
vg0223526274 sf0223520405 2 23526274 NA 2.33E-06
vg0129784098 sf0129783053 1 29784098 NA 2.36E-06
vg0224817087 sf0224811218 2 24817087 NA 3.80E-06
vg0222308618 sf0222302749 2 22308618 NA 3.80E-06