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Detailed information for vg0708022997:

Variant ID: vg0708022997 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8022997
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGGGCCCCCGATGGGCCGTCTGGCGATCGTCGGCCTGATGGGCCGGAGGGGCTTCCTCAGCCCTCGCGGGAGCGAACTTGTCAAGGCGAAGTCATCCT[C/T]
CTTCGGCAGACAGTCTTCGCCTTGCACCCTTCGCCTGAGACGCCTCTGGCCTGGCGCTACTCTTCGCCTTACGCCGTTCTTGCTCCATAGCCTACGCCAT

Reverse complement sequence

ATGGCGTAGGCTATGGAGCAAGAACGGCGTAAGGCGAAGAGTAGCGCCAGGCCAGAGGCGTCTCAGGCGAAGGGTGCAAGGCGAAGACTGTCTGCCGAAG[G/A]
AGGATGACTTCGCCTTGACAAGTTCGCTCCCGCGAGGGCTGAGGAAGCCCCTCCGGCCCATCAGGCCGACGATCGCCAGACGGCCCATCGGGGGCCCATG

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	79.20%	0.20%	5.33%	15.26%	NA
All Indica	2759	70.50%	0.30%	8.81%	20.37%	NA
All Japonica	1512	90.60%	0.00%	0.40%	8.99%	NA
Aus	269	94.80%	0.00%	0.37%	4.83%	NA
Indica I	595	58.20%	0.50%	9.75%	31.60%	NA
Indica II	465	74.00%	0.00%	6.24%	19.78%	NA
Indica III	913	73.70%	0.30%	9.31%	16.65%	NA
Indica Intermediate	786	74.20%	0.30%	9.03%	16.54%	NA
Temperate Japonica	767	85.40%	0.00%	0.52%	14.08%	NA
Tropical Japonica	504	98.00%	0.00%	0.20%	1.79%	NA
Japonica Intermediate	241	91.70%	0.00%	0.41%	7.88%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	1.10%	2.22%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0708022997	C -> DEL	N	N	silent_mutation	Average:65.369; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg0708022997	C -> T	LOC_Os07g14050.1	upstream_gene_variant ; 3354.0bp to feature; MODIFIER	silent_mutation	Average:65.369; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg0708022997	C -> T	LOC_Os07g14060.1	upstream_gene_variant ; 449.0bp to feature; MODIFIER	silent_mutation	Average:65.369; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg0708022997	C -> T	LOC_Os07g14070.1	upstream_gene_variant ; 547.0bp to feature; MODIFIER	silent_mutation	Average:65.369; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg0708022997	C -> T	LOC_Os07g14060-LOC_Os07g14070	intergenic_region ; MODIFIER	silent_mutation	Average:65.369; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708022997	2.08E-07	2.08E-07	mr1300	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