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Detailed information for vg1215896444:

Variant ID: vg1215896444 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15896444
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGATATGGGTGGGTTATTTTCGCTGCAGAAAAAAAACACATGAATTTTTCATGTTTGTATGCCATCTACGTTTTTTTAAAGATAATGAAAATGGATTA[C/G]
ATATCCGGTCTCTGCCCGTGGGCACACAACCAAACAAATTACACTCTTTTCGTGAAGAAACATTTTTCTAACACAGGAGAAAAACAATGTTAAAAACATT

Reverse complement sequence

AATGTTTTTAACATTGTTTTTCTCCTGTGTTAGAAAAATGTTTCTTCACGAAAAGAGTGTAATTTGTTTGGTTGTGTGCCCACGGGCAGAGACCGGATAT[G/C]
TAATCCATTTTCATTATCTTTAAAAAAACGTAGATGGCATACAAACATGAAAAATTCATGTGTTTTTTTTCTGCAGCGAAAATAACCCACCCATATCATG

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	89.60%	1.30%	0.34%	8.82%	NA
All Indica	2759	93.70%	0.10%	0.25%	5.98%	NA
All Japonica	1512	84.20%	3.80%	0.40%	11.64%	NA
Aus	269	72.90%	0.00%	1.12%	26.02%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	76.30%	0.00%	0.86%	22.80%	NA
Indica III	913	97.50%	0.00%	0.00%	2.52%	NA
Indica Intermediate	786	94.80%	0.30%	0.38%	4.58%	NA
Temperate Japonica	767	96.10%	3.50%	0.13%	0.26%	NA
Tropical Japonica	504	67.30%	0.20%	0.99%	31.55%	NA
Japonica Intermediate	241	81.70%	12.00%	0.00%	6.22%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	1.10%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215896444	C -> DEL	N	N	silent_mutation	Average:18.931; most accessible tissue: Callus, score: 62.42	N	N	N	N
vg1215896444	C -> G	LOC_Os12g27096.1	upstream_gene_variant ; 3148.0bp to feature; MODIFIER	silent_mutation	Average:18.931; most accessible tissue: Callus, score: 62.42	N	N	N	N
vg1215896444	C -> G	LOC_Os12g27102.1	intron_variant ; MODIFIER	silent_mutation	Average:18.931; most accessible tissue: Callus, score: 62.42	N	N	N	N
vg1215896444	C -> G	LOC_Os12g27102.2	intron_variant ; MODIFIER	silent_mutation	Average:18.931; most accessible tissue: Callus, score: 62.42	N	N	N	N
vg1215896444	C -> G	LOC_Os12g27102.3	intron_variant ; MODIFIER	silent_mutation	Average:18.931; most accessible tissue: Callus, score: 62.42	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215896444	1.55E-06	NA	mr1023_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
vg1215896444	1.41E-07	NA	mr1079_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1215896444	NA	8.45E-06	mr1113_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1215896444	3.10E-06	NA	mr1489_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