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Detailed information for vg0913675210:

Variant ID: vg0913675210 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13675210
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

AAGATGATGCCCCGACTGGTTTTCAAGACCATCGCAAGGAACTCAACCACATCTTTGGCGGACCCCTGGCTTATGAATCCAAGAGAAAGCAAAAGCTGAC[C/T]
GAACGGGAGATCAATGTTGTCCAGCCCGACACACCTCAATATCTTCGGTAGTCAGAGACAACAATCAAGTTCGACCGCTCGGATCATCCCGACCGAGTGG

Reverse complement sequence

CCACTCGGTCGGGATGATCCGAGCGGTCGAACTTGATTGTTGTCTCTGACTACCGAAGATATTGAGGTGTGTCGGGCTGGACAACATTGATCTCCCGTTC[G/A]
GTCAGCTTTTGCTTTCTCTTGGATTCATAAGCCAGGGGTCCGCCAAAGATGTGGTTGAGTTCCTTGCGATGGTCTTGAAAACCAGTCGGGGCATCATCTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.40%	5.60%	0.00%	0.00%	NA
All Indica	2759	95.40%	4.60%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	54.60%	45.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	91.20%	8.80%	0.00%	0.00%	NA
Indica III	913	94.90%	5.10%	0.00%	0.00%	NA
Indica Intermediate	786	95.00%	5.00%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0913675210	C -> T	LOC_Os09g23120.1	synonymous_variant ; p.Thr628Thr; LOW	synonymous_codon	Average:54.095; most accessible tissue: Minghui63 flag leaf, score: 77.153	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913675210	3.52E-07	NA	Heading_date	Ind_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