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 mr1079 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
vg1215869969 sf1215867265 12 15869969 1.95E-144 2.73E-52
vg1215968758 sf1215966054 12 15968758 2.85E-141 5.03E-52
vg1210219854 sf1210217266 12 10219854 4.49E-74 2.01E-07
vg1212938220 sf1212935559 12 12938220 4.28E-65 4.69E-08
vg1209186897 sf1209184306 12 9186897 9.48E-63 7.41E-08
vg1224007541 sf1223973994 12 24007541 5.34E-57 NA
vg0217071443 sf0217065573 2 17071443 1.64E-52 NA
vg1223898851 sf1223865304 12 23898851 9.34E-52 1.44E-08
vg1215871396 sf1215868692 12 15871396 NA 2.27E-27
vg0610620315 sf0610619316 6 10620315 NA 3.95E-12
vg1215966147 sf1215963443 12 15966147 NA 3.46E-11
vg1215976560 sf1215973856 12 15976560 NA 5.65E-11
vg1215970855 sf1215968151 12 15970855 NA 1.31E-10
vg1216165822 sf1216163118 12 16165822 NA 5.41E-10
vg0218141493 sf0218135624 2 18141493 NA 1.88E-08
vg1216492299 sf1216489592 12 16492299 NA 8.40E-08
vg0233789179 sf0233783310 2 33789179 NA 1.65E-07
vg1216284064 sf1216281360 12 16284064 NA 2.71E-07
vg0102116003 sf0102115003 1 2116003 NA 3.72E-07
vg0432732386 sf0432547273 4 32732386 NA 4.85E-07
vg0106845118 sf0106844118 1 6845118 NA 5.96E-07
vg1216413575 sf1216410868 12 16413575 NA 6.15E-07
vg1215220184 sf1215217481 12 15220184 NA 6.61E-07
vg1216151894 sf1216149190 12 16151894 NA 6.87E-07
vg1216414409 sf1216411702 12 16414409 NA 8.34E-07
vg0918927566 sf0918926566 9 18927566 NA 1.31E-06
vg1216358136 sf1216355432 12 16358136 NA 1.47E-06
vg0710900579 sf0710899585 7 10900579 NA 8.76E-06