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Detailed information for vg0800993769:

Variant ID: vg0800993769 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 993769
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTTCATCCTAACCATTACAAGCAAGACATTGTATGAAGAGGGGCGAACATGCAGATTGATAAACTGACGCGTGGTGGACAAGAATCACCAATTTGTGAC[C/T]
GGTCTGACACTGGTCATGTCGTCAGCAGACAGCCATGTTCCCACGTCGCGCCTGCTTCCGGCGGAAGTGGAGGTAGGTATGGGTCGTCCCATCAGAAGGT

Reverse complement sequence

ACCTTCTGATGGGACGACCCATACCTACCTCCACTTCCGCCGGAAGCAGGCGCGACGTGGGAACATGGCTGTCTGCTGACGACATGACCAGTGTCAGACC[G/A]
GTCACAAATTGGTGATTCTTGTCCACCACGCGTCAGTTTATCAATCTGCATGTTCGCCCCTCTTCATACAATGTCTTGCTTGTAATGGTTAGGATGAAGC

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	89.90%	0.90%	3.20%	5.99%	NA
All Indica	2759	87.50%	0.00%	2.54%	9.97%	NA
All Japonica	1512	93.30%	2.90%	3.51%	0.33%	NA
Aus	269	91.40%	0.00%	8.55%	0.00%	NA
Indica I	595	85.70%	0.00%	2.69%	11.60%	NA
Indica II	465	83.00%	0.00%	4.09%	12.90%	NA
Indica III	913	91.80%	0.00%	1.64%	6.57%	NA
Indica Intermediate	786	86.50%	0.00%	2.54%	10.94%	NA
Temperate Japonica	767	89.00%	5.20%	5.35%	0.39%	NA
Tropical Japonica	504	98.80%	0.00%	1.19%	0.00%	NA
Japonica Intermediate	241	95.00%	1.70%	2.49%	0.83%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	93.30%	0.00%	3.33%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0800993769	C -> T	LOC_Os08g02470.1	upstream_gene_variant ; 610.0bp to feature; MODIFIER	silent_mutation	Average:28.682; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0800993769	C -> T	LOC_Os08g02460-LOC_Os08g02470	intergenic_region ; MODIFIER	silent_mutation	Average:28.682; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0800993769	C -> DEL	N	N	silent_mutation	Average:28.682; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0800993769	9.67E-07	9.67E-07	mr1181_2	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