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Detailed information for vg0806948099:

Variant ID: vg0806948099 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6948099
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCGGAACGTCGGAAACTAAAGCAATTAAACAAAAATCAACAAAACAGTACAAAAACAAGCATAAACAGTACATGTGGATAATTTTAACATGTAGATCTT[A/G]
ATTTTAGAAAAATTTAGCAACTTGAACTACCTGAAACGGATCTACGGTTATTTAGTTATGATTTTCCGAAGTTTTAATCTATTAGAAAATCGGAAAAAAG

Reverse complement sequence

CTTTTTTCCGATTTTCTAATAGATTAAAACTTCGGAAAATCATAACTAAATAACCGTAGATCCGTTTCAGGTAGTTCAAGTTGCTAAATTTTTCTAAAAT[T/C]
AAGATCTACATGTTAAAATTATCCACATGTACTGTTTATGCTTGTTTTTGTACTGTTTTGTTGATTTTTGTTTAATTGCTTTAGTTTCCGACGTTCCGGA

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	61.40%	1.60%	13.27%	23.66%	NA
All Indica	2759	48.00%	0.10%	17.04%	34.90%	NA
All Japonica	1512	87.70%	4.90%	1.46%	5.95%	NA
Aus	269	54.60%	0.00%	42.01%	3.35%	NA
Indica I	595	60.30%	0.20%	7.73%	31.76%	NA
Indica II	465	49.00%	0.00%	14.84%	36.13%	NA
Indica III	913	38.30%	0.00%	23.22%	38.44%	NA
Indica Intermediate	786	49.10%	0.30%	18.19%	32.44%	NA
Temperate Japonica	767	81.20%	9.60%	1.43%	7.69%	NA
Tropical Japonica	504	95.60%	0.00%	1.98%	2.38%	NA
Japonica Intermediate	241	91.70%	0.00%	0.41%	7.88%	NA
VI/Aromatic	96	53.10%	0.00%	11.46%	35.42%	NA
Intermediate	90	63.30%	0.00%	12.22%	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
vg0806948099	A -> G	LOC_Os08g11850.1	downstream_gene_variant ; 1227.0bp to feature; MODIFIER	silent_mutation	Average:30.833; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0806948099	A -> G	LOC_Os08g11840-LOC_Os08g11850	intergenic_region ; MODIFIER	silent_mutation	Average:30.833; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0806948099	A -> DEL	N	N	silent_mutation	Average:30.833; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806948099	NA	1.42E-07	mr1162	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
vg0806948099	2.01E-06	3.25E-06	mr1517	Jap_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
vg0806948099	2.68E-06	NA	mr1844	Jap_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
vg0806948099	NA	2.53E-13	mr1900	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
vg0806948099	NA	1.96E-10	mr1905	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
vg0806948099	NA	2.08E-07	mr1915	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
vg0806948099	NA	5.82E-08	mr1004_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
vg0806948099	NA	2.82E-08	mr1205_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
vg0806948099	NA	3.90E-07	mr1302_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
vg0806948099	NA	5.84E-07	mr1824_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
vg0806948099	NA	1.23E-13	mr1838_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
vg0806948099	NA	3.00E-06	mr1928_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