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Detailed information for vg0700969178:

Variant ID: vg0700969178 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 969178
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAATTCTAGAGATTTGGTTCAGGGCCATAGATTTCTCATCAAGTTTCAAAAGCATGTGTGTTTCTAATTGACCAGTCTGCACACTAGACAACGCTATGG[C/T]
CTTCTGTTATACTCCCTCCATACTCGTAAAGGAAGTTGTTTAGGACAATGTTTAAGCCAAACCTTGGGAATATAAATCATGAATAACTCTTAAGTTGTTG

Reverse complement sequence

CAACAACTTAAGAGTTATTCATGATTTATATTCCCAAGGTTTGGCTTAAACATTGTCCTAAACAACTTCCTTTACGAGTATGGAGGGAGTATAACAGAAG[G/A]
CCATAGCGTTGTCTAGTGTGCAGACTGGTCAATTAGAAACACACATGCTTTTGAAACTTGATGAGAAATCTATGGCCCTGAACCAAATCTCTAGAATTTT

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	73.30%	26.70%	0.06%	0.00%	NA
All Indica	2759	54.90%	45.00%	0.11%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	47.40%	52.60%	0.00%	0.00%	NA
Indica II	465	90.50%	9.20%	0.22%	0.00%	NA
Indica III	913	32.20%	67.70%	0.11%	0.00%	NA
Indica Intermediate	786	65.90%	34.00%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0700969178	C -> T	LOC_Os07g02690.1	upstream_gene_variant ; 3690.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700969178	C -> T	LOC_Os07g02674.1	intron_variant ; 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
vg0700969178	NA	6.78E-08	mr1731	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
vg0700969178	NA	8.03E-08	mr1739	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
vg0700969178	NA	2.87E-06	mr1970_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