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Detailed information for vg1215794097:

Variant ID: vg1215794097 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15794097
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTTCGTCGGTCGGCCGAATTCCACAATAGTCCCGGTTGCAATAAAAACCGGGGCTAAAGATCACTAAAGATGATCTTTAGTCCCGGTTAAAAAGGGTA[A/C]
CGGGCATATTTGATCTTTAGTCCCGGTTGGTAACACCAACCGGGACTAAAGATCCCGATTCAAATGCTGTCAAGGCCTATCAAGCCCCCCCCCCCCCCCC

Reverse complement sequence

GGGGGGGGGGGGGGGGCTTGATAGGCCTTGACAGCATTTGAATCGGGATCTTTAGTCCCGGTTGGTGTTACCAACCGGGACTAAAGATCAAATATGCCCG[T/G]
TACCCTTTTTAACCGGGACTAAAGATCATCTTTAGTGATCTTTAGCCCCGGTTTTTATTGCAACCGGGACTATTGTGGAATTCGGCCGACCGACGAAAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.00%	7.80%	1.27%	0.00%	NA
All Indica	2759	97.90%	1.20%	0.87%	0.00%	NA
All Japonica	1512	80.70%	17.70%	1.59%	0.00%	NA
Aus	269	93.70%	5.90%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	90.80%	5.20%	4.09%	0.00%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	98.90%	0.60%	0.51%	0.00%	NA
Temperate Japonica	767	96.10%	3.40%	0.52%	0.00%	NA
Tropical Japonica	504	56.00%	40.70%	3.37%	0.00%	NA
Japonica Intermediate	241	83.40%	15.40%	1.24%	0.00%	NA
VI/Aromatic	96	46.90%	42.70%	10.42%	0.00%	NA
Intermediate	90	88.90%	10.00%	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
vg1215794097	A -> C	LOC_Os12g26960.1	downstream_gene_variant ; 4934.0bp to feature; MODIFIER	silent_mutation	Average:29.992; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N
vg1215794097	A -> C	LOC_Os12g26970.1	intron_variant ; MODIFIER	silent_mutation	Average:29.992; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215794097	2.28E-06	3.86E-09	mr1364_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