RiceVarMap2

Detailed information for vg1127724083:

Variant ID: vg1127724083 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 27724083

Reference Allele: T

Alternative Allele: A

Primary Allele: T

Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGGAAATGATCCCCAACTCTGACCGCTCGGAGAGCCCGCTCATCCTAACCTGATCTGATGCCTTCAGCTTCTAGGTTCAGTAATCCCTCTCTTCTTCGC[T/A]
TCAGTGATTTATCTAATGCCTTCAACTGCTATTCAGTAATCCCTCTCTAGCTTTGTTTGCTTCAGTGATTTCAATTTTATTATTTGCTTCTGTTCAGCAG

Reverse complement sequence

CTGCTGAACAGAAGCAAATAATAAAATTGAAATCACTGAAGCAAACAAAGCTAGAGAGGGATTACTGAATAGCAGTTGAAGGCATTAGATAAATCACTGA[A/T]
GCGAAGAAGAGAGGGATTACTGAACCTAGAAGCTGAAGGCATCAGATCAGGTTAGGATGAGCGGGCTCTCCGAGCGGTCAGAGTTGGGGATCATTTCCAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.80%	1.80%	5.46%	28.97%	NA
All Indica	2759	61.60%	2.70%	6.85%	28.89%	NA
All Japonica	1512	75.50%	0.60%	3.70%	20.17%	NA
Aus	269	28.30%	0.70%	1.86%	69.14%	NA
Indica I	595	61.80%	0.20%	4.20%	33.78%	NA
Indica II	465	65.60%	0.00%	2.37%	32.04%	NA
Indica III	913	64.00%	4.30%	10.73%	21.03%	NA
Indica Intermediate	786	56.20%	4.30%	7.00%	32.44%	NA
Temperate Japonica	767	81.20%	1.20%	1.69%	15.91%	NA
Tropical Japonica	504	62.30%	0.00%	7.94%	29.76%	NA
Japonica Intermediate	241	85.10%	0.00%	1.24%	13.69%	NA
VI/Aromatic	96	33.30%	1.00%	1.04%	64.58%	NA
Intermediate	90	71.10%	0.00%	7.78%	21.11%	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
vg1127724083	T -> A	LOC_Os11g45820.1	5_prime_UTR_variant ; 161.0bp to feature; MODIFIER	silent_mutation	Average:51.074; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg1127724083	T -> A	LOC_Os11g45809.1	downstream_gene_variant ; 2983.0bp to feature; MODIFIER	silent_mutation	Average:51.074; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg1127724083	T -> DEL	N	N	silent_mutation	Average:51.074; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg1127724083:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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