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Detailed information for vg1107364083:

Variant ID: vg1107364083 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7364083
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.06, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGCTTTACTTAGGGCCCGATTGAGATAGAATCATCCGTGACGGCCGTTTGCCTGATTAAGATAGATCTTTACATCAGTGACTTCTAGCCTGTGACGGA[T/C]
GCTATGCCCGATTGAGATGGGGCTTACCGCCCGATTGAGATGAGGGTATCCGTTCTAGTGATCTACTTTGGTGGCCTTCATATGTCACTTCGTTTATGAT

Reverse complement sequence

ATCATAAACGAAGTGACATATGAAGGCCACCAAAGTAGATCACTAGAACGGATACCCTCATCTCAATCGGGCGGTAAGCCCCATCTCAATCGGGCATAGC[A/G]
TCCGTCACAGGCTAGAAGTCACTGATGTAAAGATCTATCTTAATCAGGCAAACGGCCGTCACGGATGATTCTATCTCAATCGGGCCCTAAGTAAAGCCCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.70%	26.80%	10.62%	22.94%	NA
All Indica	2759	6.70%	40.00%	17.65%	35.70%	NA
All Japonica	1512	92.00%	2.80%	0.20%	4.96%	NA
Aus	269	61.00%	37.50%	0.37%	1.12%	NA
Indica I	595	3.70%	28.90%	9.75%	57.65%	NA
Indica II	465	1.90%	34.40%	31.61%	32.04%	NA
Indica III	913	7.90%	55.60%	17.52%	18.95%	NA
Indica Intermediate	786	10.30%	33.50%	15.52%	40.71%	NA
Temperate Japonica	767	96.50%	0.40%	0.13%	3.00%	NA
Tropical Japonica	504	90.30%	2.60%	0.20%	6.94%	NA
Japonica Intermediate	241	81.30%	11.20%	0.41%	7.05%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	46.70%	20.00%	12.22%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107364083	T -> DEL	N	N	silent_mutation	Average:26.38; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg1107364083	T -> C	LOC_Os11g13440.1	upstream_gene_variant ; 1015.0bp to feature; MODIFIER	silent_mutation	Average:26.38; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg1107364083	T -> C	LOC_Os11g13430.1	downstream_gene_variant ; 4479.0bp to feature; MODIFIER	silent_mutation	Average:26.38; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N
vg1107364083	T -> C	LOC_Os11g13430-LOC_Os11g13440	intergenic_region ; MODIFIER	silent_mutation	Average:26.38; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107364083	1.28E-06	3.22E-13	mr1781_2	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