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Detailed information for vg1121730562:

Variant ID: vg1121730562 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21730562
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTGTCGAGGATTGTTCTAGCATCCATCCAGCCCATGGCCGACTTCTCACCAAGATATTTATTCAACATCAGGCCAAACACATTGGTGTCCACTAAGGT[C/A]
CTGTTTGGTTCCATGGGCTAATGTTTAGCCCTCACCTTTTAGCCTCAAATTAGCCCTCAAGGATCCAAACAGGTGGGCTAATTTTGAGCTAATATGAATT

Reverse complement sequence

AATTCATATTAGCTCAAAATTAGCCCACCTGTTTGGATCCTTGAGGGCTAATTTGAGGCTAAAAGGTGAGGGCTAAACATTAGCCCATGGAACCAAACAG[G/T]
ACCTTAGTGGACACCAATGTGTTTGGCCTGATGTTGAATAAATATCTTGGTGAGAAGTCGGCCATGGGCTGGATGGATGCTAGAACAATCCTCGACACAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.70%	0.50%	3.68%	11.11%	NA
All Indica	2759	80.00%	0.00%	4.93%	15.01%	NA
All Japonica	1512	96.60%	1.50%	0.53%	1.39%	NA
Aus	269	80.70%	0.00%	7.43%	11.90%	NA
Indica I	595	63.20%	0.20%	17.98%	18.66%	NA
Indica II	465	78.10%	0.00%	2.37%	19.57%	NA
Indica III	913	88.90%	0.00%	0.99%	10.08%	NA
Indica Intermediate	786	83.60%	0.00%	1.15%	15.27%	NA
Temperate Japonica	767	95.40%	3.00%	1.04%	0.52%	NA
Tropical Japonica	504	97.60%	0.00%	0.00%	2.38%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	42.70%	0.00%	8.33%	48.96%	NA
Intermediate	90	84.40%	1.10%	2.22%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121730562	C -> A	LOC_Os11g36820.1	synonymous_variant ; p.Val202Val; LOW	synonymous_codon	Average:52.69; most accessible tissue: Minghui63 panicle, score: 90.184	N	N	N	N
vg1121730562	C -> DEL	LOC_Os11g36820.1	N	frameshift_variant	Average:52.69; most accessible tissue: Minghui63 panicle, score: 90.184	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121730562	2.07E-07	2.57E-09	Awn_length	Jap_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