Search for Variation information by Variation ID:

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

Detailed information for vg1008957832:

Variant ID: vg1008957832 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8957832
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGAGGCGATGTACATGGGCAACAATGGGTACCGTCCACAAGGAGGTCAGGGGTGGAACCAACCACGCCCATATTATCAAGGAGGTAACAACAACGGTAA[C/T]
TTTTCTAACCAGCCCTCCTTGAAGGATCTCGTTTTTGCGCAAGCTAAAACCACTAATGCGCTAAGCAAAATGCTTGTTGCCAATGACAAGATCCTAGAGA

Reverse complement sequence

TCTCTAGGATCTTGTCATTGGCAACAAGCATTTTGCTTAGCGCATTAGTGGTTTTAGCTTGCGCAAAAACGAGATCCTTCAAGGAGGGCTGGTTAGAAAA[G/A]
TTACCGTTGTTGTTACCTCCTTGATAATATGGGCGTGGTTGGTTCCACCCCTGACCTCCTTGTGGACGGTACCCATTGTTGCCCATGTACATCGCCTCCT

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	25.20%	0.10%	15.32%	59.35%	NA
All Indica	2759	9.20%	0.20%	19.86%	70.75%	NA
All Japonica	1512	58.90%	0.10%	6.28%	34.72%	NA
Aus	269	3.00%	0.00%	11.90%	85.13%	NA
Indica I	595	7.90%	0.70%	14.29%	77.14%	NA
Indica II	465	8.60%	0.20%	27.53%	63.66%	NA
Indica III	913	8.40%	0.00%	20.04%	71.52%	NA
Indica Intermediate	786	11.50%	0.00%	19.34%	69.21%	NA
Temperate Japonica	767	88.70%	0.00%	0.39%	10.95%	NA
Tropical Japonica	504	13.90%	0.20%	16.87%	69.05%	NA
Japonica Intermediate	241	58.50%	0.00%	2.90%	38.59%	NA
VI/Aromatic	96	11.50%	0.00%	33.33%	55.21%	NA
Intermediate	90	30.00%	0.00%	18.89%	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
vg1008957832	C -> T	LOC_Os10g17724.1	synonymous_variant ; p.Asn86Asn; LOW	synonymous_codon	Average:18.73; most accessible tissue: Callus, score: 35.341	N	N	N	N
vg1008957832	C -> DEL	LOC_Os10g17724.1	N	frameshift_variant	Average:18.73; most accessible tissue: Callus, score: 35.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1008957832	2.84E-06	2.83E-06	mr1335_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