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 mr1877 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
vg1111147450 sf1111141767 11 11147450 7.48E-08 7.48E-08
vg0425095758 sf0424910619 4 25095758 2.29E-07 2.29E-07
vg0218635577 sf0218629708 2 18635577 2.94E-07 2.94E-07
vg0900843381 sf0900842381 9 843381 4.69E-07 4.69E-07
vg0717412492 sf0717411499 7 17412492 4.70E-07 4.70E-07
vg0124420479 sf0124419435 1 24420479 5.52E-07 5.52E-07
vg0729408499 sf0729407507 7 29408499 7.12E-07 7.12E-07
vg0430121316 sf0429936187 4 30121316 7.22E-07 7.22E-07
vg0606307778 sf0606306779 6 6307778 7.48E-07 7.48E-07
vg0317442324 sf0317441106 3 17442324 7.65E-07 7.65E-07
vg0111858180 sf0111857154 1 11858180 1.21E-06 1.21E-06
vg0506828905 sf0506828847 5 6828905 1.32E-06 1.32E-06
vg0128444157 sf0128443112 1 28444157 1.57E-06 1.57E-06
vg1213044906 sf1213042245 12 13044906 1.85E-06 1.85E-06
vg0506994489 sf0506994431 5 6994489 1.97E-06 1.97E-06
vg0615233212 sf0615232213 6 15233212 2.41E-06 2.41E-06
vg0719003857 sf0719002864 7 19003857 2.41E-06 2.41E-06
vg1011329733 sf1011258553 10 11329733 2.44E-06 2.44E-06
vg0610540066 sf0610539067 6 10540066 2.44E-06 2.44E-06
vg0322431668 sf0322430157 3 22431668 2.92E-06 2.92E-06
vg0806930067 sf0806929072 8 6930067 3.22E-06 3.22E-06
vg0616962035 sf0616961038 6 16962035 6.56E-06 6.56E-06