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Detailed information for vg0628658970:

Variant ID: vg0628658970 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 28658970
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

GATTTTATGCTGGTCAGAACTATCTCGACTATCTCGACTACATTCAAAACTATATGCAACTAGTATATTTTCCCATGGGTTGCAACAGTTCTCAAACAAT[G/C]
ATAGAAGACACATGGCATAAGTTCTAGCCCTGCATAATTACTCATAAATAAAAGATAACCGTTCTCTAATTCAATGAATCACATGCATGATTCACAAAAG

Reverse complement sequence

CTTTTGTGAATCATGCATGTGATTCATTGAATTAGAGAACGGTTATCTTTTATTTATGAGTAATTATGCAGGGCTAGAACTTATGCCATGTGTCTTCTAT[C/G]
ATTGTTTGAGAACTGTTGCAACCCATGGGAAAATATACTAGTTGCATATAGTTTTGAATGTAGTCGAGATAGTCGAGATAGTTCTGACCAGCATAAAATC

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	71.10%	28.60%	0.23%	0.02%	NA
All Indica	2759	52.60%	47.00%	0.33%	0.04%	NA
All Japonica	1512	98.70%	1.30%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	67.40%	32.40%	0.17%	0.00%	NA
Indica II	465	32.70%	66.50%	0.86%	0.00%	NA
Indica III	913	52.00%	47.60%	0.33%	0.00%	NA
Indica Intermediate	786	53.90%	45.80%	0.13%	0.13%	NA
Temperate Japonica	767	97.50%	2.30%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	65.60%	33.30%	1.11%	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
vg0628658970	G -> C	LOC_Os06g47270.1	downstream_gene_variant ; 4727.0bp to feature; MODIFIER	silent_mutation	Average:56.328; most accessible tissue: Callus, score: 87.522	N	N	N	N
vg0628658970	G -> C	LOC_Os06g47280.1	downstream_gene_variant ; 1991.0bp to feature; MODIFIER	silent_mutation	Average:56.328; most accessible tissue: Callus, score: 87.522	N	N	N	N
vg0628658970	G -> C	LOC_Os06g47294.1	downstream_gene_variant ; 4515.0bp to feature; MODIFIER	silent_mutation	Average:56.328; most accessible tissue: Callus, score: 87.522	N	N	N	N
vg0628658970	G -> C	LOC_Os06g47290.1	intron_variant ; MODIFIER	silent_mutation	Average:56.328; most accessible tissue: Callus, score: 87.522	N	N	N	N
vg0628658970	G -> DEL	N	N	silent_mutation	Average:56.328; most accessible tissue: Callus, score: 87.522	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0628658970	NA	1.79E-07	mr1321_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
vg0628658970	2.67E-06	3.83E-08	mr1974_2	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
vg0628658970	1.33E-06	2.78E-07	mr1974_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