Search for Variation information by Variation ID:

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

Detailed information for vg0615088126:

Variant ID: vg0615088126 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 15088126
Reference Allele: A	Alternative Allele: G,AGCCGGTCGGTGAGGATGTAGGCGCCCAACAACAGCGGCATAATAGGCCGGCCATGCAAGCGGAAACACCAGTCGGCGGCGGACGAGGCG
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTACTCCTTGTAATTGGACCAGCTATATCAAGTGTAGCTTCATTTGGAGATGAGTGAATGCTAGGAATGTCTTCATTAACTAGTCGGCGGCGGACGAGGC[A/G,AGCCGGTCGGTGAGGATGTAGGCGCCCAACAACAGCGGCATAATAGGCCGGCCATGCAAGCGGAAACACCAGTCGGCGGCGGACGAGGCG]
GCCGGTCGGTGAGGATGTAGACGCCCAACAACGGCGGCATAATAGGCCAGCCATGCAGGCGGAAACACCAGTCGGCGGCGGACGAGGCGACCGGTCGGTG

Reverse complement sequence

CACCGACCGGTCGCCTCGTCCGCCGCCGACTGGTGTTTCCGCCTGCATGGCTGGCCTATTATGCCGCCGTTGTTGGGCGTCTACATCCTCACCGACCGGC[T/C,CGCCTCGTCCGCCGCCGACTGGTGTTTCCGCTTGCATGGCCGGCCTATTATGCCGCTGTTGTTGGGCGCCTACATCCTCACCGACCGGCT]
GCCTCGTCCGCCGCCGACTAGTTAATGAAGACATTCCTAGCATTCACTCATCTCCAAATGAAGCTACACTTGATATAGCTGGTCCAATTACAAGGAGTAG

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	36.80%	2.40%	52.35%	8.44%	AGCCGGTCGGTGAGGATGTAGGCGCCCAACAACAGCGGCATAATAGGCCGGCCATGCAAGCGGAAACACCAGTCGGCGGCGGACGAGGCG: 0.02%
All Indica	2759	9.50%	3.80%	81.26%	5.44%	AGCCGGTCGGTGAGGATGTAGGCGCCCAACAACAGCGGCATAATAGGCCGGCCATGCAAGCGGAAACACCAGTCGGCGGCGGACGAGGCG: 0.04%
All Japonica	1512	92.30%	0.30%	7.14%	0.20%	NA
Aus	269	1.50%	1.50%	28.62%	68.40%	NA
Indica I	595	12.60%	1.00%	75.97%	10.42%	NA
Indica II	465	10.10%	0.90%	82.37%	6.67%	NA
Indica III	913	6.40%	8.00%	84.56%	0.99%	AGCCGGTCGGTGAGGATGTAGGCGCCCAACAACAGCGGCATAATAGGCCGGCCATGCAAGCGGAAACACCAGTCGGCGGCGGACGAGGCG: 0.11%
Indica Intermediate	786	10.40%	2.70%	80.79%	6.11%	NA
Temperate Japonica	767	97.40%	0.10%	2.48%	0.00%	NA
Tropical Japonica	504	84.30%	0.80%	14.68%	0.20%	NA
Japonica Intermediate	241	92.90%	0.00%	6.22%	0.83%	NA
VI/Aromatic	96	26.00%	0.00%	19.79%	54.17%	NA
Intermediate	90	56.70%	1.10%	31.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0615088126	A -> G	LOC_Os06g25830.1	missense_variant ; p.Cys182Arg; MODERATE	nonsynonymous_codon ; C182R	Average:31.048; most accessible tissue: Minghui63 panicle, score: 53.77	unknown	unknown	TOLERATED	0.85
vg0615088126	A -> AGCCGGTCGGTGAGGATGTAGGCGCCCAAC AACAGCGGCATAATAGGCCGGCCATGCAAG CGGAAACACCAGTCGGCGGCGGACGAGGCG	LOC_Os06g25830.1	frameshift_variant ; p.Cys182fs; HIGH	frameshift_variant	Average:31.048; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0615088126	A -> DEL	LOC_Os06g25830.1	N	frameshift_variant	Average:31.048; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0615088126	NA	1.54E-06	mr1881	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