Search for Variation information by Variation ID:

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

Detailed information for vg0913083924:

Variant ID: vg0913083924 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13083924
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTCAAAATGCATGGTCCAGTGCTCCTTGTTCTCCGCGGGGGTATCCTCCTGGCACTCGGTCCATTCGGCGACAAAATCAACTAACACTTGGGACTTGAT[T/C]
GAAATTCTGGGCTTGAATGATATGTCCAAAGACATCAACTCCAAAGCCCACTTAGCAATACGTCCGTTTGCTTCGCGATTGTGCAGTATGTCACCGAGTG

Reverse complement sequence

CACTCGGTGACATACTGCACAATCGCGAAGCAAACGGACGTATTGCTAAGTGGGCTTTGGAGTTGATGTCTTTGGACATATCATTCAAGCCCAGAATTTC[A/G]
ATCAAGTCCCAAGTGTTAGTTGATTTTGTCGCCGAATGGACCGAGTGCCAGGAGGATACCCCCGCGGAGAACAAGGAGCACTGGACCATGCATTTTGACG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.70%	0.10%	21.54%	20.69%	NA
All Indica	2759	51.40%	0.00%	20.33%	28.31%	NA
All Japonica	1512	65.90%	0.30%	27.31%	6.48%	NA
Aus	269	68.40%	0.00%	10.78%	20.82%	NA
Indica I	595	32.80%	0.00%	22.18%	45.04%	NA
Indica II	465	60.20%	0.00%	20.00%	19.78%	NA
Indica III	913	55.20%	0.00%	22.56%	22.23%	NA
Indica Intermediate	786	55.70%	0.00%	16.54%	27.74%	NA
Temperate Japonica	767	86.20%	0.30%	8.87%	4.69%	NA
Tropical Japonica	504	45.40%	0.20%	46.63%	7.74%	NA
Japonica Intermediate	241	44.40%	0.40%	45.64%	9.54%	NA
VI/Aromatic	96	60.40%	1.00%	3.12%	35.42%	NA
Intermediate	90	76.70%	0.00%	13.33%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0913083924	T -> DEL	LOC_Os09g21610.1	N	frameshift_variant	Average:10.302; most accessible tissue: Callus, score: 23.306	N	N	N	N
vg0913083924	T -> C	LOC_Os09g21610.1	synonymous_variant ; p.Ser1411Ser; LOW	synonymous_codon	Average:10.302; most accessible tissue: Callus, score: 23.306	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913083924	NA	6.44E-06	mr1378_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
vg0913083924	6.65E-07	3.29E-07	mr1546_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