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Detailed information for vg0222023649:

Variant ID: vg0222023649 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22023649
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATATCACCGTCGATTTTCACTTAAATTGGTGAACCTAGTATTTTAGACCATTAGATTAGATGTATTTTATTTTAAAAACACCCTATTACTCTATTACT[A/C]
TATGTACGTATACGGGAAACATAAGTAGTCAGTACGTGCATACAACCTGGAAAAAGAAACGAAGTTTACCCACTGTCCTTCGGAACCAAGAAAAATCTAC

Reverse complement sequence

GTAGATTTTTCTTGGTTCCGAAGGACAGTGGGTAAACTTCGTTTCTTTTTCCAGGTTGTATGCACGTACTGACTACTTATGTTTCCCGTATACGTACATA[T/G]
AGTAATAGAGTAATAGGGTGTTTTTAAAATAAAATACATCTAATCTAATGGTCTAAAATACTAGGTTCACCAATTTAAGTGAAAATCGACGGTGATATTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.60%	0.20%	0.17%	0.00%	NA
All Indica	2759	99.50%	0.30%	0.18%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	98.90%	0.40%	0.74%	0.00%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.50%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0222023649	A -> C	LOC_Os02g36470.1	upstream_gene_variant ; 2430.0bp to feature; MODIFIER	N	Average:24.024; most accessible tissue: Callus, score: 53.051	N	N	N	N
vg0222023649	A -> C	LOC_Os02g36460.1	downstream_gene_variant ; 2671.0bp to feature; MODIFIER	N	Average:24.024; most accessible tissue: Callus, score: 53.051	N	N	N	N
vg0222023649	A -> C	LOC_Os02g36460-LOC_Os02g36470	intergenic_region ; MODIFIER	N	Average:24.024; most accessible tissue: Callus, score: 53.051	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222023649	NA	6.14E-09	Awn_length	Ind_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
vg0222023649	NA	2.03E-39	mr1124	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
vg0222023649	1.11E-06	1.45E-07	mr1619	Ind_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
vg0222023649	NA	2.16E-06	mr1915_2	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