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 mr1142 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 6.79E-165 2.54E-56
vg1215968758 sf1215966054 12 15968758 1.54E-153 5.42E-51
vg1210219854 sf1210217266 12 10219854 1.21E-87 1.21E-07
vg1210217896 sf1210215308 12 10217896 1.94E-86 4.42E-08
vg1212938220 sf1212935559 12 12938220 3.68E-73 2.74E-08
vg1224007541 sf1223973994 12 24007541 6.23E-72 NA
vg0217071443 sf0217065573 2 17071443 4.13E-71 NA
vg1215871396 sf1215868692 12 15871396 NA 1.79E-25
vg1215970855 sf1215968151 12 15970855 NA 7.02E-14
vg1215894346 sf1215891642 12 15894346 NA 1.41E-11
vg1215978234 sf1215975530 12 15978234 NA 1.86E-11
vg0610620315 sf0610619316 6 10620315 NA 2.07E-11
vg1216212155 sf1216209451 12 16212155 NA 7.64E-10
vg0218132013 sf0218126144 2 18132013 NA 1.27E-09
vg1223877720 sf1223844173 12 23877720 NA 2.37E-08
vg0901048761 sf0901047761 9 1048761 NA 3.84E-08
vg1215808919 sf1215806216 12 15808919 NA 6.41E-08
vg0102116003 sf0102115003 1 2116003 NA 7.13E-08
vg1216413575 sf1216410868 12 16413575 NA 8.20E-08
vg1216082180 sf1216079476 12 16082180 NA 9.60E-08
vg1216492299 sf1216489592 12 16492299 NA 1.34E-07
vg0918927566 sf0918926566 9 18927566 NA 1.62E-07
vg1216411230 sf1216408523 12 16411230 NA 2.76E-07
vg0106845118 sf0106844118 1 6845118 NA 2.88E-07
vg1216414409 sf1216411702 12 16414409 NA 3.69E-07
vg1216284064 sf1216281360 12 16284064 NA 7.17E-07
vg1215271479 sf1215268777 12 15271479 NA 7.58E-07
vg1216465707 sf1216463000 12 16465707 NA 9.10E-07