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 mr1750 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
vg0801625057 sf0801624059 8 1625057 3.38E-10 9.54E-09
vg0206203920 sf0206203920 2 6203920 4.08E-09 4.20E-06
vg1119545646 sf1119079334 11 19545646 4.26E-09 6.95E-06
vg0627078208 sf0627077211 6 27078208 7.23E-09 2.26E-06
vg1208272715 sf1208270121 12 8272715 8.94E-09 1.46E-06
vg1208814713 sf1208812120 12 8814713 9.35E-09 2.75E-07
vg1208272321 sf1208269727 12 8272321 9.99E-09 1.04E-08
vg0824212610 sf0824209896 8 24212610 1.43E-08 9.94E-09
vg0101087393 sf0101086393 1 1087393 2.65E-08 1.14E-09
vg1218339498 sf1218310934 12 18339498 2.86E-08 5.24E-08
vg0321972978 sf0321971485 3 21972978 3.37E-08 3.56E-08
vg0504195192 sf0504195169 5 4195192 4.36E-08 2.06E-07
vg1006880582 sf1006896205 10 6880582 6.29E-08 4.29E-07
vg0141267197 sf0141266154 1 41267197 7.08E-08 2.01E-07
vg0205800449 sf0205800449 2 5800449 8.36E-08 2.63E-09
vg0209742252 sf0209742250 2 9742252 1.95E-07 1.01E-07
vg0623519091 sf0623518094 6 23519091 5.91E-07 1.61E-11
vg0506871977 sf0506871919 5 6871977 7.72E-07 1.96E-07
vg0223219897 sf0223214028 2 23219897 7.98E-07 2.52E-07
vg0140957424 sf0140956381 1 40957424 3.27E-06 1.18E-08
vg0143166899 sf0143165855 1 43166899 NA 3.17E-10
vg1008926715 sf1008855576 10 8926715 NA 1.00E-08
vg0233793468 sf0233787599 2 33793468 NA 4.24E-07
vg0137184767 sf0137183724 1 37184767 NA 4.50E-07