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Detailed information for vg1205661778:

Variant ID: vg1205661778 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5661778
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCAATGGATTCTCCAGAAGTGTTGAATCTTCGTAGAGGAACCAAACTCGAATGTCTTTTTGGAAACCGTCATAAAAACTGCAGAACCAGTCCTTGAGCA[G/A]
CTCGGCCGATAGCTTTGCTCCTGCATCGGCTGGCGTGGAGGCATATTCTCCGTAAGATGTGCATCTACGATGAGTGCGTTCTTCTCCATCATCATCTACA

Reverse complement sequence

TGTAGATGATGATGGAGAAGAACGCACTCATCGTAGATGCACATCTTACGGAGAATATGCCTCCACGCCAGCCGATGCAGGAGCAAAGCTATCGGCCGAG[C/T]
TGCTCAAGGACTGGTTCTGCAGTTTTTATGACGGTTTCCAAAAAGACATTCGAGTTTGGTTCCTCTACGAAGATTCAACACTTCTGGAGAATCCATTGGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.60%	39.00%	0.44%	0.00%	NA
All Indica	2759	94.90%	4.50%	0.69%	0.00%	NA
All Japonica	1512	3.60%	96.40%	0.00%	0.00%	NA
Aus	269	60.20%	39.40%	0.37%	0.00%	NA
Indica I	595	97.00%	2.40%	0.67%	0.00%	NA
Indica II	465	96.60%	3.40%	0.00%	0.00%	NA
Indica III	913	94.60%	4.10%	1.31%	0.00%	NA
Indica Intermediate	786	92.50%	7.10%	0.38%	0.00%	NA
Temperate Japonica	767	5.00%	95.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.60%	97.40%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	31.10%	67.80%	1.11%	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
vg1205661778	G -> A	LOC_Os12g10610.1	upstream_gene_variant ; 2329.0bp to feature; MODIFIER	silent_mutation	Average:38.486; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1205661778	G -> A	LOC_Os12g10604.1	downstream_gene_variant ; 4604.0bp to feature; MODIFIER	silent_mutation	Average:38.486; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1205661778	G -> A	LOC_Os12g10620.1	downstream_gene_variant ; 455.0bp to feature; MODIFIER	silent_mutation	Average:38.486; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1205661778	G -> A	LOC_Os12g10610-LOC_Os12g10620	intergenic_region ; MODIFIER	silent_mutation	Average:38.486; 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
vg1205661778	3.16E-07	3.16E-07	mr1335_2	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