Search for Variation information by Variation ID:

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

Detailed information for vg1000877655:

Variant ID: vg1000877655 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 877655
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGGAGATATGGAAAAGAATCCGGATAGTTTCTGACCGTTTCAAATTTCTACCGGATACTGGTCTTAATTACCATATCTCGTCTTTCCAAATTTGTTTCC[A/G]
TTTAAAAAAAACTATCTGTACTCATTTTCAAATCCGGTACTATAAAAAAAAAATCTATTCGAGACTATCCGTTTCTAAAATACGTGCGGGTATCGGAAAC

Reverse complement sequence

GTTTCCGATACCCGCACGTATTTTAGAAACGGATAGTCTCGAATAGATTTTTTTTTTATAGTACCGGATTTGAAAATGAGTACAGATAGTTTTTTTTAAA[T/C]
GGAAACAAATTTGGAAAGACGAGATATGGTAATTAAGACCAGTATCCGGTAGAAATTTGAAACGGTCAGAAACTATCCGGATTCTTTTCCATATCTCCAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.10%	4.40%	0.21%	1.21%	NA
All Indica	2759	98.70%	0.50%	0.07%	0.76%	NA
All Japonica	1512	94.70%	5.10%	0.07%	0.13%	NA
Aus	269	44.20%	41.60%	2.60%	11.52%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	99.60%	0.00%	0.00%	0.43%	NA
Indica III	913	99.10%	0.30%	0.00%	0.55%	NA
Indica Intermediate	786	97.20%	0.80%	0.25%	1.78%	NA
Temperate Japonica	767	90.40%	9.60%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	98.30%	0.80%	0.00%	0.83%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	91.10%	7.80%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000877655	A -> G	LOC_Os10g02400.1	downstream_gene_variant ; 3313.0bp to feature; MODIFIER	silent_mutation	Average:34.652; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1000877655	A -> G	LOC_Os10g02410.1	downstream_gene_variant ; 2707.0bp to feature; MODIFIER	silent_mutation	Average:34.652; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1000877655	A -> G	LOC_Os10g02400-LOC_Os10g02410	intergenic_region ; MODIFIER	silent_mutation	Average:34.652; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1000877655	A -> DEL	N	N	silent_mutation	Average:34.652; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000877655	1.31E-06	NA	mr1210	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
vg1000877655	8.91E-06	NA	mr1585	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
vg1000877655	8.43E-07	NA	mr1586	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
vg1000877655	NA	3.70E-06	mr1586	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
vg1000877655	4.92E-07	NA	mr1765	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
vg1000877655	NA	4.36E-06	mr1765	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