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 mr1068 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
vg0610584620 sf0610583621 6 10584620 1.14E-14 1.14E-14
vg0616129303 sf0616128305 6 16129303 2.62E-09 2.62E-09
vg0403922278 sf0403917884 4 3922278 2.91E-09 2.91E-09
vg1001052701 sf1001051677 10 1052701 8.58E-09 8.59E-09
vg0402677786 sf0402673390 4 2677786 1.63E-08 1.63E-08
vg0609938604 sf0609937605 6 9938604 8.41E-08 8.41E-08
vg1126292021 sf1125820434 11 26292021 2.31E-07 2.31E-07
vg1117172234 sf1116706086 11 17172234 5.76E-07 5.77E-07
vg1125622211 sf1125156050 11 25622211 6.38E-07 6.38E-07
vg1123359940 sf1122893810 11 23359940 6.55E-07 6.56E-07
vg0433587363 sf0433402247 4 33587363 9.93E-07 9.93E-07
vg0610489279 sf0610488280 6 10489279 1.00E-06 1.00E-06
vg1222716971 sf1222683410 12 22716971 1.48E-06 1.48E-06
vg0414121081 sf0414111796 4 14121081 2.48E-06 2.48E-06
vg1208212432 sf1208209837 12 8212432 3.08E-06 3.08E-06
vg0409862324 sf0409853022 4 9862324 3.56E-06 3.56E-06
vg0900715492 sf0900714492 9 715492 4.62E-06 4.62E-06
vg0727786940 sf0727785947 7 27786940 4.62E-06 4.63E-06
vg1209876216 sf1209873626 12 9876216 8.17E-06 8.17E-06