Search for Variation information by Variation ID:

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

Detailed information for vg0614036522:

Variant ID: vg0614036522 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14036522
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGTCTCCGCCTGCACGGCTGGCCTATTATGCCACCGTTGTTGGGCGTCTACGTCTTCACCGACCGGCTTGCCTTCGCCGCCGCCGACTGGTATCTCCGC[T/C]
TGCACGGCTGGCCTATTATGCGCCGTTTGTTGGGCGTCTACGCTTTCACCGACCGGCTTGCCTTCGCCGCCGCCGACTGGTATCTCCGCCTGTACGGCTG

Reverse complement sequence

CAGCCGTACAGGCGGAGATACCAGTCGGCGGCGGCGAAGGCAAGCCGGTCGGTGAAAGCGTAGACGCCCAACAAACGGCGCATAATAGGCCAGCCGTGCA[A/G]
GCGGAGATACCAGTCGGCGGCGGCGAAGGCAAGCCGGTCGGTGAAGACGTAGACGCCCAACAACGGTGGCATAATAGGCCAGCCGTGCAGGCGGAGACAC

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	33.70%	2.70%	11.74%	51.80%	NA
All Indica	2759	3.80%	0.40%	16.75%	79.05%	NA
All Japonica	1512	91.40%	0.00%	1.32%	7.28%	NA
Aus	269	2.20%	39.40%	13.01%	45.35%	NA
Indica I	595	3.90%	0.70%	18.99%	76.47%	NA
Indica II	465	2.60%	0.20%	26.88%	70.32%	NA
Indica III	913	2.20%	0.10%	8.54%	89.16%	NA
Indica Intermediate	786	6.40%	0.60%	18.58%	74.43%	NA
Temperate Japonica	767	96.50%	0.00%	0.91%	2.61%	NA
Tropical Japonica	504	82.90%	0.00%	2.18%	14.88%	NA
Japonica Intermediate	241	92.90%	0.00%	0.83%	6.22%	NA
VI/Aromatic	96	61.50%	5.20%	22.92%	10.42%	NA
Intermediate	90	46.70%	7.80%	17.78%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0614036522	T -> C	LOC_Os06g24030.1	synonymous_variant ; p.Leu55Leu; LOW	synonymous_codon	Average:32.311; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg0614036522	T -> DEL	LOC_Os06g24030.1	N	frameshift_variant	Average:32.311; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614036522	NA	4.60E-09	mr1644	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
vg0614036522	NA	5.08E-11	mr1986_2	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