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Detailed information for vg1107849096:

Variant ID: vg1107849096 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7849096
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAAAAGCAATATGAAAAGAACGATTCGATTGATTGATAGTAGATTTTTTTTCTTACAATGAACCGGCCTTGTCCCTTATATAGGGGTTGGTCTTGCCTT[A/C]
TACAGGCCCTCCTCCACATCCAACTCGGGGTAGAATCCAAAGGAAACCCGAAACATGCATTCCCGAGCAAGGAAACTTCGAGACCCGACGAAACAGGGTT

Reverse complement sequence

AACCCTGTTTCGTCGGGTCTCGAAGTTTCCTTGCTCGGGAATGCATGTTTCGGGTTTCCTTTGGATTCTACCCCGAGTTGGATGTGGAGGAGGGCCTGTA[T/G]
AAGGCAAGACCAACCCCTATATAAGGGACAAGGCCGGTTCATTGTAAGAAAAAAAATCTACTATCAATCAATCGAATCGTTCTTTTCATATTGCTTTTAG

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	56.70%	2.10%	8.15%	33.01%	NA
All Indica	2759	32.30%	0.10%	12.98%	54.62%	NA
All Japonica	1512	92.00%	6.30%	0.66%	0.99%	NA
Aus	269	89.60%	0.00%	4.09%	6.32%	NA
Indica I	595	75.10%	0.00%	2.35%	22.52%	NA
Indica II	465	14.00%	0.00%	10.11%	75.91%	NA
Indica III	913	13.80%	0.30%	22.23%	63.64%	NA
Indica Intermediate	786	32.10%	0.10%	11.96%	55.85%	NA
Temperate Japonica	767	91.00%	8.20%	0.65%	0.13%	NA
Tropical Japonica	504	96.00%	0.20%	0.99%	2.78%	NA
Japonica Intermediate	241	86.70%	13.30%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	71.10%	0.00%	6.67%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107849096	A -> DEL	N	N	silent_mutation	Average:31.959; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1107849096	A -> C	LOC_Os11g14090.1	upstream_gene_variant ; 441.0bp to feature; MODIFIER	silent_mutation	Average:31.959; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1107849096	A -> C	LOC_Os11g14090-LOC_Os11g14110	intergenic_region ; MODIFIER	silent_mutation	Average:31.959; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107849096	3.72E-06	3.72E-06	mr1317	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