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 mr1695 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
vg0307366875 sf0307365873 3 7366875 8.69E-66 NA
vg0821337222 sf0821334509 8 21337222 1.82E-64 NA
vg0713531449 sf0713530456 7 13531449 3.28E-63 NA
vg0803251090 sf0803250093 8 3251090 5.27E-63 NA
vg0232319173 sf0232313304 2 32319173 9.15E-63 NA
vg0332876688 sf0332869558 3 32876688 4.07E-59 2.24E-07
vg0822783342 sf0822780629 8 22783342 1.61E-58 NA
vg0610086748 sf0610085749 6 10086748 NA 8.51E-17
vg0610128100 sf0610127101 6 10128100 NA 2.71E-16
vg0610884163 sf0610883164 6 10884163 NA 7.64E-14
vg0619510251 sf0619509254 6 19510251 NA 1.42E-10
vg0610205177 sf0610204178 6 10205177 NA 1.90E-10
vg0610596670 sf0610595671 6 10596670 NA 2.80E-10
vg0610284244 sf0610283245 6 10284244 NA 4.97E-10
vg0610573007 sf0610572008 6 10573007 NA 7.50E-10
vg0609889578 sf0609888579 6 9889578 NA 3.31E-08
vg0609993621 sf0609992622 6 9993621 NA 4.02E-08
vg1216541381 sf1216538674 12 16541381 NA 4.89E-08
vg0613280734 sf0613279735 6 13280734 NA 7.00E-08
vg0609897017 sf0609896018 6 9897017 NA 1.13E-07
vg0610023723 sf0610022724 6 10023723 NA 2.08E-07
vg0621037715 sf0621036718 6 21037715 NA 2.10E-07
vg0610069455 sf0610068456 6 10069455 NA 2.37E-07
vg0403070551 sf0403066155 4 3070551 NA 3.18E-07
vg0610397337 sf0610396338 6 10397337 NA 3.94E-07
vg0610137001 sf0610136002 6 10137001 NA 5.35E-07
vg0803532236 sf0803531239 8 3532236 NA 6.30E-07
vg1205369570 sf1205368556 12 5369570 NA 7.76E-07
vg0404302990 sf0404298596 4 4302990 NA 8.55E-07
vg0621039858 sf0621038861 6 21039858 NA 9.37E-07
vg0610191856 sf0610190857 6 10191856 NA 1.05E-06
vg0610137789 sf0610136790 6 10137789 NA 1.20E-06
vg0423388047 sf0423202902 4 23388047 NA 4.11E-06