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Detailed information for vg0906920907:

Variant ID: vg0906920907 (JBrowse)	Variation Type: INDEL
Chromosome: chr09	Position: 6920907
Reference Allele: A	Alternative Allele: G,ACGATTGTACTATAATTACATCTG,ACGATTGTACTATGATTACATCTG
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAATGATTCAAAATTACGTGAAACTTACATATAAGTTACACTGTAGTTACATACAAATTACAGTGTAATTACACTACGATTGTACTATAATTACATCT[A/G,ACGATTGTACTATAATTACATCTG,ACGATTGTACTATGATTACATCTG]
TCAAATTTTTAGGAGAAAAATTGTCGAGAAATATATAGGTGGTCCCTAAAACAAAGTAAATAAGGTGTGGTTCATCTGGCCCTTCACACATTAGATACAG

Reverse complement sequence

CTGTATCTAATGTGTGAAGGGCCAGATGAACCACACCTTATTTACTTTGTTTTAGGGACCACCTATATATTTCTCGACAATTTTTCTCCTAAAAATTTGA[T/C,CAGATGTAATTATAGTACAATCGT,CAGATGTAATCATAGTACAATCGT]
AGATGTAATTATAGTACAATCGTAGTGTAATTACACTGTAATTTGTATGTAACTACAGTGTAACTTATATGTAAGTTTCACGTAATTTTGAATCATTAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.00%	10.20%	1.93%	16.34%	ACGATTGTACTATAATTACATCTG: 0.49%; ACGATTGTACTATGATTACATCTG: 0.02%
All Indica	2759	85.60%	0.60%	1.52%	12.07%	ACGATTGTACTATAATTACATCTG: 0.22%
All Japonica	1512	46.80%	29.50%	2.18%	21.49%	NA
Aus	269	62.50%	0.70%	3.72%	26.77%	ACGATTGTACTATAATTACATCTG: 6.32%
Indica I	595	95.50%	1.30%	1.01%	2.18%	NA
Indica II	465	97.80%	0.40%	0.22%	1.29%	ACGATTGTACTATAATTACATCTG: 0.22%
Indica III	913	69.00%	0.10%	2.08%	28.59%	ACGATTGTACTATAATTACATCTG: 0.22%
Indica Intermediate	786	90.10%	0.80%	2.04%	6.74%	ACGATTGTACTATAATTACATCTG: 0.38%
Temperate Japonica	767	26.20%	53.30%	2.22%	18.25%	NA
Tropical Japonica	504	68.80%	0.20%	2.38%	28.57%	NA
Japonica Intermediate	241	66.40%	14.90%	1.66%	17.01%	NA
VI/Aromatic	96	57.30%	5.20%	0.00%	36.46%	ACGATTGTACTATGATTACATCTG: 1.04%
Intermediate	90	71.10%	14.40%	6.67%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906920907	A -> G	LOC_Os09g12210.1	downstream_gene_variant ; 2057.0bp to feature; MODIFIER	silent_mutation	Average:25.691; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0906920907	A -> G	LOC_Os09g12210-LOC_Os09g12220	intergenic_region ; MODIFIER	silent_mutation	Average:25.691; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0906920907	A -> DEL	N	N	silent_mutation	Average:25.691; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0906920907	A -> ACGATTGTACTATAATTACATCTG	LOC_Os09g12210.1	downstream_gene_variant ; 2058.0bp to feature; MODIFIER	silent_mutation	Average:25.691; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0906920907	A -> ACGATTGTACTATAATTACATCTG	LOC_Os09g12210-LOC_Os09g12220	intergenic_region ; MODIFIER	silent_mutation	Average:25.691; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0906920907	A -> ACGATTGTACTATGATTACATCTG	LOC_Os09g12210.1	downstream_gene_variant ; 2058.0bp to feature; MODIFIER	silent_mutation	Average:25.691; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0906920907	A -> ACGATTGTACTATGATTACATCTG	LOC_Os09g12210-LOC_Os09g12220	intergenic_region ; MODIFIER	silent_mutation	Average:25.691; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906920907	NA	9.11E-13	Plant_height	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0906920907	1.10E-06	1.38E-15	Spikelet_length	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0906920907	NA	1.66E-12	Spikelet_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0906920907	NA	4.98E-06	mr1010	Jap_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
vg0906920907	NA	6.10E-06	mr1775	Jap_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
vg0906920907	NA	1.68E-06	mr1977	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
vg0906920907	NA	4.70E-06	mr1977	Jap_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