Search for Variation information by Variation ID:

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

Detailed information for vg1216246100:

Variant ID: vg1216246100 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 16246100
Reference Allele: A	Alternative Allele: G,AG
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACAATTACTGTTCAAGGTGACTTTGACCCGGCACTTCTCTTCATCACGATCATGAGGAATCTGGGCATACAAAGGGGCAGTCCCAAATCCTATGAGGAA[A/G,AG]
GACATCGTACGCAACTCTTGGACAAATCCTTCAGTACCAAACAAGTACTCAGGCTTGTAGCACAGCATCTAAAGACAAGTGAAAGGAGGGAGTTAAGTCA

Reverse complement sequence

TGACTTAACTCCCTCCTTTCACTTGTCTTTAGATGCTGTGCTACAAGCCTGAGTACTTGTTTGGTACTGAAGGATTTGTCCAAGAGTTGCGTACGATGTC[T/C,CT]
TTCCTCATAGGATTTGGGACTGCCCCTTTGTATGCCCAGATTCCTCATGATCGTGATGAAGAGAAGTGCCGGGTCAAAGTCACCTTGAACAGTAATTGTG

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	32.40%	3.70%	47.82%	15.95%	AG: 0.06%
All Indica	2759	11.50%	5.90%	72.49%	9.97%	AG: 0.11%
All Japonica	1512	66.10%	0.10%	3.24%	30.56%	NA
Aus	269	31.60%	4.10%	61.34%	2.97%	NA
Indica I	595	17.10%	2.50%	66.39%	13.78%	AG: 0.17%
Indica II	465	11.80%	5.40%	61.94%	20.86%	NA
Indica III	913	5.60%	9.00%	82.04%	3.40%	NA
Indica Intermediate	786	14.00%	5.20%	72.26%	8.27%	AG: 0.25%
Temperate Japonica	767	95.70%	0.00%	0.78%	3.52%	NA
Tropical Japonica	504	16.30%	0.20%	6.15%	77.38%	NA
Japonica Intermediate	241	75.90%	0.40%	4.98%	18.67%	NA
VI/Aromatic	96	83.30%	0.00%	13.54%	3.12%	NA
Intermediate	90	56.70%	0.00%	36.67%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216246100	A -> DEL	LOC_Os12g27600.1	N	frameshift_variant	Average:19.244; most accessible tissue: Minghui63 young leaf, score: 23.613	N	N	N	N
vg1216246100	A -> AG	LOC_Os12g27600.1	frameshift_variant ; p.Leu85fs; HIGH	frameshift_variant	Average:19.244; most accessible tissue: Minghui63 young leaf, score: 23.613	N	N	N	N
vg1216246100	A -> G	LOC_Os12g27600.1	synonymous_variant ; p.Ser83Ser; LOW	synonymous_codon	Average:19.244; most accessible tissue: Minghui63 young leaf, score: 23.613	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216246100	1.75E-06	NA	mr1524	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