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Detailed information for vg1005377616:

Variant ID: vg1005377616 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5377616
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAAAATTAGAAAAGAAAAGGATAGTCCAAGTAGGAATACGATTTAAAAATAGCTGAAATTCGGAATTAAAAATAAGAAAAATTAAAAGAAGAGTTCATA[G/T]
AAGAACCCAATACGAGATTAATTAAAATTCAGAATAAAAATAAAAATGAAATCTGAAATTAGCAAAAAAAAGAAGAGTTAAAGTAGGAATACAATTTAAA

Reverse complement sequence

TTTAAATTGTATTCCTACTTTAACTCTTCTTTTTTTTGCTAATTTCAGATTTCATTTTTATTTTTATTCTGAATTTTAATTAATCTCGTATTGGGTTCTT[C/A]
TATGAACTCTTCTTTTAATTTTTCTTATTTTTAATTCCGAATTTCAGCTATTTTTAAATCGTATTCCTACTTGGACTATCCTTTTCTTTTCTAATTTTAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.40%	2.30%	2.98%	0.36%	NA
All Indica	2759	97.90%	0.00%	2.10%	0.00%	NA
All Japonica	1512	88.60%	6.90%	3.37%	1.12%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	95.30%	0.00%	4.71%	0.00%	NA
Indica Intermediate	786	98.50%	0.00%	1.53%	0.00%	NA
Temperate Japonica	767	80.30%	13.60%	3.91%	2.22%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	92.90%	0.00%	7.05%	0.00%	NA
VI/Aromatic	96	71.90%	3.10%	25.00%	0.00%	NA
Intermediate	90	91.10%	0.00%	8.89%	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
vg1005377616	G -> T	LOC_Os10g09930.1	upstream_gene_variant ; 2234.0bp to feature; MODIFIER	silent_mutation	Average:17.558; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1005377616	G -> T	LOC_Os10g09920-LOC_Os10g09930	intergenic_region ; MODIFIER	silent_mutation	Average:17.558; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1005377616	G -> DEL	N	N	silent_mutation	Average:17.558; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005377616	1.69E-06	2.24E-06	mr1768_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