Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1115848370:

Variant ID: vg1115848370 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15848370
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTTTAAAACTTACAACTTTTCCATCACATCAAAACTTTCCTACACACATAAACTTCCAATTTTTCCGTCACATCGTTTCAATTTCAACCGAACTTC[C/T]
AATTTTGGCGTGAACTAAACACACCCTACCTCTGTTTCGCGCGTGCGCGTGGGGGGGTGGGGGGTTAGTTTTTTCTGAGCGCATTGCTTCACAAAACCCC

Reverse complement sequence

GGGGTTTTGTGAAGCAATGCGCTCAGAAAAAACTAACCCCCCACCCCCCCACGCGCACGCGCGAAACAGAGGTAGGGTGTGTTTAGTTCACGCCAAAATT[G/A]
GAAGTTCGGTTGAAATTGAAACGATGTGACGGAAAAATTGGAAGTTTATGTGTGTAGGAAAGTTTTGATGTGATGGAAAAGTTGTAAGTTTTAAAAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.90%	24.90%	0.21%	0.00%	NA
All Indica	2759	59.70%	40.00%	0.33%	0.00%	NA
All Japonica	1512	99.20%	0.70%	0.07%	0.00%	NA
Aus	269	83.30%	16.70%	0.00%	0.00%	NA
Indica I	595	42.40%	57.50%	0.17%	0.00%	NA
Indica II	465	63.70%	35.90%	0.43%	0.00%	NA
Indica III	913	64.70%	35.20%	0.11%	0.00%	NA
Indica Intermediate	786	64.60%	34.70%	0.64%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.40%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	0.00%	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
vg1115848370	C -> T	LOC_Os11g27530.1	downstream_gene_variant ; 3969.0bp to feature; MODIFIER	silent_mutation	Average:41.795; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg1115848370	C -> T	LOC_Os11g27540.1	downstream_gene_variant ; 2745.0bp to feature; MODIFIER	silent_mutation	Average:41.795; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg1115848370	C -> T	LOC_Os11g27540.2	downstream_gene_variant ; 2329.0bp to feature; MODIFIER	silent_mutation	Average:41.795; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg1115848370	C -> T	LOC_Os11g27530-LOC_Os11g27540	intergenic_region ; MODIFIER	silent_mutation	Average:41.795; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115848370	1.82E-06	1.82E-06	mr1388	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