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Detailed information for vg0826635155:

Variant ID: vg0826635155 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26635155
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGACGAAATGTCAAACATTTGTCAAAAAGTCAACGGCGTCATACATTAAAATATGGAGGTAGTATCATCTTGTAGTTTGTATCATCCTAATAAATACAAT[A/G]
CATGCATCCAATAGAATTAGAGAACATGAGAGTGGAGGATTTAAAAAAGTAATAATTTCATGGAGAATGGGCCATAGTTATATTATGGAATATAAAAAAA

Reverse complement sequence

TTTTTTTATATTCCATAATATAACTATGGCCCATTCTCCATGAAATTATTACTTTTTTAAATCCTCCACTCTCATGTTCTCTAATTCTATTGGATGCATG[T/C]
ATTGTATTTATTAGGATGATACAAACTACAAGATGATACTACCTCCATATTTTAATGTATGACGCCGTTGACTTTTTGACAAATGTTTGACATTTCGTCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.20%	0.30%	11.05%	23.44%	NA
All Indica	2759	58.70%	0.30%	13.59%	27.44%	NA
All Japonica	1512	83.80%	0.00%	2.91%	13.29%	NA
Aus	269	14.90%	3.30%	36.06%	45.72%	NA
Indica I	595	49.90%	0.00%	21.85%	28.24%	NA
Indica II	465	89.00%	0.20%	0.86%	9.89%	NA
Indica III	913	40.60%	0.40%	17.52%	41.40%	NA
Indica Intermediate	786	68.40%	0.30%	10.31%	20.99%	NA
Temperate Japonica	767	95.20%	0.00%	0.26%	4.56%	NA
Tropical Japonica	504	75.20%	0.00%	4.96%	19.84%	NA
Japonica Intermediate	241	65.60%	0.00%	7.05%	27.39%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	68.90%	0.00%	6.67%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826635155	A -> G	LOC_Os08g42140.1	upstream_gene_variant ; 3076.0bp to feature; MODIFIER	silent_mutation	Average:18.129; most accessible tissue: Minghui63 root, score: 50.524	N	N	N	N
vg0826635155	A -> G	LOC_Os08g42140-LOC_Os08g42150	intergenic_region ; MODIFIER	silent_mutation	Average:18.129; most accessible tissue: Minghui63 root, score: 50.524	N	N	N	N
vg0826635155	A -> DEL	N	N	silent_mutation	Average:18.129; most accessible tissue: Minghui63 root, score: 50.524	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826635155	NA	9.41E-07	mr1070	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	6.55E-07	mr1180	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	6.11E-07	NA	mr1249	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	1.34E-06	1.34E-06	mr1249	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	1.93E-06	mr1692	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	2.23E-08	mr1739	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	4.69E-08	mr1739	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	1.35E-07	mr1839	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	3.33E-06	mr1959	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	9.42E-07	9.42E-07	mr1985	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	3.33E-06	mr1263_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	5.08E-06	mr1336_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	2.14E-06	mr1579_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	6.30E-06	mr1729_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0826635155	NA	6.33E-06	mr1759_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251