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Detailed information for vg0113605352:

Variant ID: vg0113605352 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13605352
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.02, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGGAATTTATCGCGGCGATTCAAGAATAACTCATGGGATTCATCAACGAACAAATCCTTGATCCCAAGGGTGAATTCTACTACGACAGAAATACAATT[C/G]
ATAGGTCCTTAGCTTCTGAAATAGCGACTACTACTACGTCGAAATCGTAGCTAGCTAGGACATAATGGATTGTAATTAATACATGTCTATTTTTCTATAT

Reverse complement sequence

ATATAGAAAAATAGACATGTATTAATTACAATCCATTATGTCCTAGCTAGCTACGATTTCGACGTAGTAGTAGTCGCTATTTCAGAAGCTAAGGACCTAT[G/C]
AATTGTATTTCTGTCGTAGTAGAATTCACCCTTGGGATCAAGGATTTGTTCGTTGATGAATCCCATGAGTTATTCTTGAATCGCCGCGATAAATTCCTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.00%	8.40%	9.59%	28.99%	NA
All Indica	2759	36.50%	14.10%	13.81%	35.59%	NA
All Japonica	1512	86.60%	0.00%	0.40%	12.96%	NA
Aus	269	39.00%	0.00%	17.47%	43.49%	NA
Indica I	595	36.50%	25.40%	10.08%	28.07%	NA
Indica II	465	29.70%	4.30%	15.48%	50.54%	NA
Indica III	913	38.30%	14.90%	16.43%	30.34%	NA
Indica Intermediate	786	38.30%	10.60%	12.60%	38.55%	NA
Temperate Japonica	767	98.80%	0.00%	0.00%	1.17%	NA
Tropical Japonica	504	64.90%	0.00%	0.79%	34.33%	NA
Japonica Intermediate	241	93.40%	0.00%	0.83%	5.81%	NA
VI/Aromatic	96	30.20%	1.00%	9.38%	59.38%	NA
Intermediate	90	60.00%	8.90%	11.11%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113605352	C -> G	LOC_Os01g24130.1	upstream_gene_variant ; 921.0bp to feature; MODIFIER	silent_mutation	Average:8.912; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N
vg0113605352	C -> G	LOC_Os01g24130-LOC_Os01g24140	intergenic_region ; MODIFIER	silent_mutation	Average:8.912; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N
vg0113605352	C -> DEL	N	N	silent_mutation	Average:8.912; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113605352	NA	5.36E-07	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
vg0113605352	7.04E-06	NA	mr1218_2	Ind_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
vg0113605352	NA	5.73E-06	mr1519_2	Ind_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
vg0113605352	4.50E-06	NA	mr1871_2	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