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Detailed information for vg1213938478:

Variant ID: vg1213938478 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13938478
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGAATATCTTATTTGTGTCTCGGGTTTGTTTCTCAACTTGTACATCAAGGAAATACCTTGAGACTTAGTCGGCTACGACTGTATTTTATCTGTATCTGC[C/G]
TATTCCGTTAGGGATATAGATTATCTTTTGTAACACGGACTCCTTCCCATATATAGGGGGGTCCGGGTGCCTCTAGGGGCAGAGGTTGATTTTCTCCAAA

Reverse complement sequence

TTTGGAGAAAATCAACCTCTGCCCCTAGAGGCACCCGGACCCCCCTATATATGGGAAGGAGTCCGTGTTACAAAAGATAATCTATATCCCTAACGGAATA[G/C]
GCAGATACAGATAAAATACAGTCGTAGCCGACTAAGTCTCAAGGTATTTCCTTGATGTACAAGTTGAGAAACAAACCCGAGACACAAATAAGATATTCTA

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	20.50%	0.20%	15.62%	63.67%	NA
All Indica	2759	6.70%	0.30%	19.68%	73.40%	NA
All Japonica	1512	48.90%	0.00%	7.67%	43.39%	NA
Aus	269	2.60%	1.10%	18.59%	77.70%	NA
Indica I	595	10.10%	0.00%	15.29%	74.62%	NA
Indica II	465	10.80%	0.00%	13.12%	76.13%	NA
Indica III	913	2.20%	0.40%	25.30%	72.07%	NA
Indica Intermediate	786	6.90%	0.40%	20.36%	72.39%	NA
Temperate Japonica	767	79.30%	0.00%	1.83%	18.90%	NA
Tropical Japonica	504	13.10%	0.00%	15.28%	71.63%	NA
Japonica Intermediate	241	27.40%	0.00%	10.37%	62.24%	NA
VI/Aromatic	96	6.20%	0.00%	17.71%	76.04%	NA
Intermediate	90	35.60%	0.00%	13.33%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213938478	C -> DEL	N	N	silent_mutation	Average:21.465; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1213938478	C -> G	LOC_Os12g24420.1	upstream_gene_variant ; 263.0bp to feature; MODIFIER	silent_mutation	Average:21.465; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1213938478	C -> G	LOC_Os12g24430.1	upstream_gene_variant ; 317.0bp to feature; MODIFIER	silent_mutation	Average:21.465; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1213938478	C -> G	LOC_Os12g24420-LOC_Os12g24430	intergenic_region ; MODIFIER	silent_mutation	Average:21.465; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213938478	1.13E-06	1.13E-06	mr1256	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