RiceVarMap2

Detailed information for vg1105974510:

Variant ID: vg1105974510 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 5974510

Reference Allele: G

Alternative Allele: A

Primary Allele: G

Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.62, G: 0.37, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

ATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCT[G/A]
CCTGCAGCACTAGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATCTGTGCGAGGAGTTGTGCAGCGGTGGATTCAG

Reverse complement sequence

CTGAATCCACCGCTGCACAACTCCTCGCACAGATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCTAGTGCTGCAGG[C/T]
AGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGAT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.60%	14.90%	0.74%	49.77%	NA
All Indica	2759	15.40%	17.10%	0.98%	66.51%	NA
All Japonica	1512	68.70%	13.90%	0.33%	17.06%	NA
Aus	269	17.10%	1.90%	0.74%	80.30%	NA
Indica I	595	35.50%	1.50%	0.50%	62.52%	NA
Indica II	465	14.40%	9.70%	1.94%	73.98%	NA
Indica III	913	2.60%	28.00%	0.44%	68.89%	NA
Indica Intermediate	786	15.80%	20.50%	1.40%	62.34%	NA
Temperate Japonica	767	69.20%	2.60%	0.52%	27.64%	NA
Tropical Japonica	504	64.90%	31.50%	0.20%	3.37%	NA
Japonica Intermediate	241	75.10%	12.90%	0.00%	12.03%	NA
VI/Aromatic	96	88.50%	0.00%	0.00%	11.46%	NA
Intermediate	90	41.10%	22.20%	1.11%	35.56%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105974510	G -> A	LOC_Os11g10840.1	missense_variant ; p.Cys64Tyr; MODERATE	nonsynonymous_codon ; C64Y	Average:45.682; most accessible tissue: Callus, score: 75.127	unknown	unknown	TOLERATED	1.00
vg1105974510	G -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:45.682; most accessible tissue: Callus, score: 75.127	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg1105974510:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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