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Detailed information for vg0700326410:

Variant ID: vg0700326410 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 326410
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ACTGTGTACATGCAGTATGCATCGATCGATCAGTTGCATCTATATATATATATTGCTAGGTACCATATAGTATGATGCAGCAATATAATGAATACAACAG[C/T]
AATACTATAGCTAGTCGATCGATCTCCAGCTCCTACCGCATGCATGCATGTGCATTATCGATCATAATTAGCAGGTGAGAGATATTTAATTAATTTTCTT

Reverse complement sequence

AAGAAAATTAATTAAATATCTCTCACCTGCTAATTATGATCGATAATGCACATGCATGCATGCGGTAGGAGCTGGAGATCGATCGACTAGCTATAGTATT[G/A]
CTGTTGTATTCATTATATTGCTGCATCATACTATATGGTACCTAGCAATATATATATATAGATGCAACTGATCGATCGATGCATACTGCATGTACACAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.30%	3.70%	0.00%	0.00%	NA
All Indica	2759	97.40%	2.60%	0.00%	0.00%	NA
All Japonica	1512	93.70%	6.30%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	92.60%	7.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	97.10%	2.90%	0.00%	0.00%	NA
Tropical Japonica	504	86.30%	13.70%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0700326410	C -> T	LOC_Os07g01510.1	upstream_gene_variant ; 3088.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700326410	C -> T	LOC_Os07g01520.1	upstream_gene_variant ; 327.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700326410	C -> T	LOC_Os07g01510-LOC_Os07g01520	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0700326410	3.16E-07	3.03E-07	mr1668	Jap_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