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Detailed information for vg1209753482:

Variant ID: vg1209753482 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9753482
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

GGACGGTGTGGATTGCTTCCCTATGGCGGTTGGGGGTATTACCGACCTTTCCAACCGCCATAACCGTCATTACCTGCCTATTTAAGGAGTTCACTCTCTT[C/G]
ACTTCAACACACACCTCAAGCAAGAGCTCTCTCATTTCTCTCAAGTTTAGTTTAGTAGTATCTAGCTGGTGGAATAGGAATATAGTAGTAATCAGGAGTC

Reverse complement sequence

GACTCCTGATTACTACTATATTCCTATTCCACCAGCTAGATACTACTAAACTAAACTTGAGAGAAATGAGAGAGCTCTTGCTTGAGGTGTGTGTTGAAGT[G/C]
AAGAGAGTGAACTCCTTAAATAGGCAGGTAATGACGGTTATGGCGGTTGGAAAGGTCGGTAATACCCCCAACCGCCATAGGGAAGCAATCCACACCGTCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.40%	8.80%	0.70%	4.15%	NA
All Indica	2759	78.90%	14.80%	1.16%	5.18%	NA
All Japonica	1512	97.90%	0.00%	0.07%	1.98%	NA
Aus	269	93.70%	0.00%	0.00%	6.32%	NA
Indica I	595	85.20%	14.30%	0.50%	0.00%	NA
Indica II	465	68.60%	14.00%	2.37%	15.05%	NA
Indica III	913	78.90%	16.90%	0.77%	3.50%	NA
Indica Intermediate	786	80.20%	13.20%	1.40%	5.22%	NA
Temperate Japonica	767	98.40%	0.00%	0.00%	1.56%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	92.50%	0.00%	0.41%	7.05%	NA
VI/Aromatic	96	90.60%	5.20%	0.00%	4.17%	NA
Intermediate	90	95.60%	2.20%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209753482	C -> DEL	N	N	silent_mutation	Average:58.507; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg1209753482	C -> G	LOC_Os12g17040.1	downstream_gene_variant ; 1904.0bp to feature; MODIFIER	silent_mutation	Average:58.507; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg1209753482	C -> G	LOC_Os12g17050.1	downstream_gene_variant ; 1000.0bp to feature; MODIFIER	silent_mutation	Average:58.507; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg1209753482	C -> G	LOC_Os12g17040-LOC_Os12g17050	intergenic_region ; MODIFIER	silent_mutation	Average:58.507; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209753482	3.40E-06	2.49E-06	mr1672	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