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Detailed information for vg0816331445:

Variant ID: vg0816331445 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16331445
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATATCTTCACTTGTACTATGTTTTTTTTTTAGGGTTCACTTGTATTAATTGAGGCTCTCCTAGACCCCCATTAATCCTAGGAGATAAAAAATCATGTTA[G/C]
TTGAAAATTCTTAAAATCCATAATCAAGAAAAAGAAAAATATCTTGATCATTTAATGTACACAAAAAACGCAACTAAAAAATATGAGATTGGATCAACAA

Reverse complement sequence

TTGTTGATCCAATCTCATATTTTTTAGTTGCGTTTTTTGTGTACATTAAATGATCAAGATATTTTTCTTTTTCTTGATTATGGATTTTAAGAATTTTCAA[C/G]
TAACATGATTTTTTATCTCCTAGGATTAATGGGGGTCTAGGAGAGCCTCAATTAATACAAGTGAACCCTAAAAAAAAAACATAGTACAAGTGAAGATATC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.20%	7.60%	0.23%	0.02%	NA
All Indica	2759	98.60%	1.40%	0.00%	0.00%	NA
All Japonica	1512	84.50%	14.80%	0.60%	0.07%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	97.70%	2.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	73.30%	25.60%	1.04%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	88.00%	11.60%	0.41%	0.00%	NA
VI/Aromatic	96	17.70%	80.20%	2.08%	0.00%	NA
Intermediate	90	84.40%	15.60%	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
vg0816331445	G -> C	LOC_Os08g26850.1	downstream_gene_variant ; 316.0bp to feature; MODIFIER	silent_mutation	Average:33.122; most accessible tissue: Callus, score: 67.522	N	N	N	N
vg0816331445	G -> C	LOC_Os08g26840-LOC_Os08g26850	intergenic_region ; MODIFIER	silent_mutation	Average:33.122; most accessible tissue: Callus, score: 67.522	N	N	N	N
vg0816331445	G -> DEL	N	N	silent_mutation	Average:33.122; most accessible tissue: Callus, score: 67.522	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816331445	5.50E-11	3.65E-29	Awn_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
vg0816331445	NA	4.26E-10	Awn_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