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 mr1055 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
vg1215977007 sf1215974303 12 15977007 7.51E-187 6.88E-98
vg1210219854 sf1210217266 12 10219854 1.66E-76 2.06E-06
vg1215958324 sf1215955620 12 15958324 1.60E-71 9.63E-19
vg1224007541 sf1223973994 12 24007541 5.07E-70 NA
vg0217066401 sf0217060531 2 17066401 5.35E-63 NA
vg1213439429 sf1213436767 12 13439429 1.40E-57 NA
vg1215871396 sf1215868692 12 15871396 NA 1.49E-45
vg1215970855 sf1215968151 12 15970855 NA 5.44E-25
vg1216212155 sf1216209451 12 16212155 NA 1.61E-13
vg1216151894 sf1216149190 12 16151894 NA 1.86E-13
vg1216346285 sf1216343581 12 16346285 NA 1.14E-12
vg1216001107 sf1215998403 12 16001107 NA 1.06E-11
vg1215261373 sf1215258671 12 15261373 NA 1.31E-11
vg1121327044 sf1120860921 11 21327044 NA 1.69E-11
vg1215780845 sf1215778142 12 15780845 NA 3.94E-11
vg1216165057 sf1216162353 12 16165057 NA 4.45E-11
vg1215321806 sf1215319104 12 15321806 NA 6.41E-11
vg1121306839 sf1120840717 11 21306839 NA 1.21E-10
vg1216413575 sf1216410868 12 16413575 NA 1.28E-10
vg0610620315 sf0610619316 6 10620315 NA 1.38E-10
vg1216062863 sf1216060159 12 16062863 NA 1.89E-10
vg1217302353 sf1217296308 12 17302353 NA 2.93E-10
vg1215962650 sf1215959946 12 15962650 NA 3.00E-10
vg0920348485 sf0920348004 9 20348485 NA 3.73E-10
vg0521485463 sf0521422904 5 21485463 NA 1.21E-09
vg1216530604 sf1216527897 12 16530604 NA 1.85E-09
vg1215438933 sf1215436231 12 15438933 NA 3.74E-09