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 mr1042 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
vg1105925054 sf1105920806 11 5925054 1.35E-11 1.43E-06
vg1105906564 sf1105902316 11 5906564 9.45E-11 1.07E-06
vg1219173044 sf1219144514 12 19173044 1.07E-10 NA
vg1221504344 sf1221470891 12 21504344 7.60E-09 NA
vg1019043595 sf1018972152 10 19043595 2.10E-08 NA
vg0133176308 sf0133175264 1 33176308 2.23E-08 NA
vg0712504949 sf0712503956 7 12504949 6.88E-07 3.30E-06
vg1209997382 sf1209994793 12 9997382 1.13E-06 NA
vg1000868638 sf1000867614 10 868638 4.56E-06 5.15E-06
vg0715317227 sf0715316234 7 15317227 NA 1.88E-06
vg1003735001 sf1003733978 10 3735001 NA 4.90E-06