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 mr1170 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
vg0206245186 sf0206245186 2 6245186 8.28E-18 1.20E-07
vg0206231967 sf0206231967 2 6231967 3.86E-16 1.93E-09
vg1119935565 sf1119469488 11 19935565 5.30E-14 NA
vg1227096317 sf1227062716 12 27096317 6.29E-14 NA
vg0514155166 sf0514097710 5 14155166 1.63E-13 NA
vg0608071648 sf0608070649 6 8071648 2.02E-13 NA
vg0723948342 sf0723947348 7 23948342 1.56E-12 2.40E-07
vg0205952833 sf0205952833 2 5952833 1.19E-11 3.64E-06
vg0607991416 sf0607990417 6 7991416 1.67E-10 1.64E-07
vg0608010653 sf0608009654 6 8010653 2.74E-10 1.75E-06
vg0232755756 sf0232749887 2 32755756 1.75E-08 2.63E-09
vg0142589694 sf0142588650 1 42589694 5.62E-08 NA
vg0716284413 sf0716283420 7 16284413 7.94E-08 8.96E-09
vg0206260893 sf0206260893 2 6260893 NA 1.06E-07
vg0205949239 sf0205949239 2 5949239 NA 6.98E-07
vg0206228771 sf0206228771 2 6228771 NA 8.02E-07
vg0607990166 sf0607989167 6 7990166 NA 1.71E-06
vg0616750117 sf0616749119 6 16750117 NA 2.07E-06
vg0205930978 sf0205930978 2 5930978 NA 2.75E-06
vg0613866615 sf0613865616 6 13866615 NA 4.72E-06
vg0231313596 sf0231307727 2 31313596 NA 5.97E-06
vg1128827845 sf1128304624 11 28827845 NA 7.02E-06