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 mr1154 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
vg0917918788 sf0917917787 9 17918788 1.16E-56 NA
vg0914885058 sf0914884057 9 14885058 6.56E-56 NA
vg0815683508 sf0815680794 8 15683508 6.69E-56 4.30E-07
vg0815688098 sf0815685384 8 15688098 3.54E-55 3.79E-07
vg0132881992 sf0132880948 1 32881992 1.06E-54 NA
vg1227329375 sf1227295775 12 27329375 4.73E-54 NA
vg0229949816 sf0229943947 2 29949816 1.28E-52 NA
vg0130670983 sf0130669939 1 30670983 NA 3.06E-15
vg1115489572 sf1115025885 11 15489572 NA 2.22E-10
vg1115509243 sf1115045556 11 15509243 NA 6.00E-10
vg0130813657 sf0130812613 1 30813657 NA 2.91E-09
vg1115484688 sf1115021001 11 15484688 NA 2.91E-09
vg0131033386 sf0131032342 1 31033386 NA 1.29E-08
vg0135821566 sf0135820523 1 35821566 NA 5.81E-07
vg0139928356 sf0139927313 1 39928356 NA 1.14E-06
vg1110447272 sf1110441817 11 10447272 NA 1.50E-06
vg1126531026 sf1126059441 11 26531026 NA 1.80E-06
vg0432523363 sf0432338255 4 32523363 NA 2.02E-06
vg0726380549 sf0726379555 7 26380549 NA 2.77E-06
vg0113048025 sf0113046999 1 13048025 NA 3.25E-06
vg0401697946 sf0401693495 4 1697946 NA 3.31E-06
vg1115402655 sf1114938967 11 15402655 NA 3.40E-06
vg0413709145 sf0413699859 4 13709145 NA 3.48E-06
vg1226927430 sf1226893829 12 26927430 NA 3.85E-06
vg0818200735 sf0818198022 8 18200735 NA 4.09E-06
vg1111902205 sf1111896522 11 11902205 NA 4.15E-06
vg0905354568 sf0905353568 9 5354568 NA 4.80E-06
vg1115418543 sf1114954855 11 15418543 NA 4.89E-06