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 mr1647 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
vg0714760963 sf0714759970 7 14760963 5.48E-37 NA
vg0723989329 sf0723988335 7 23989329 9.35E-37 NA
vg1226043015 sf1226009409 12 26043015 1.24E-36 NA
vg0211628824 sf0211628820 2 11628824 1.36E-36 NA
vg1014789603 sf1014718369 10 14789603 2.02E-36 NA
vg1218022526 sf1217993962 12 18022526 NA 1.70E-09
vg0119895987 sf0119894942 1 19895987 NA 5.18E-07
vg0327873390 sf0327866444 3 27873390 NA 1.19E-06
vg1217862267 sf1217833701 12 17862267 NA 1.45E-06
vg0601155306 sf0601154307 6 1155306 NA 2.27E-06
vg1218043542 sf1218014978 12 18043542 NA 2.38E-06
vg0517141494 sf0517081135 5 17141494 NA 2.69E-06
vg1218068686 sf1218040122 12 18068686 NA 3.50E-06
vg1216728644 sf1216722598 12 16728644 NA 3.72E-06
vg0327951721 sf0327944775 3 27951721 NA 4.37E-06
vg1114436354 sf1113972671 11 14436354 NA 9.20E-06