RiceVarMap2

Detailed information for vg1127723916:

Variant ID: vg1127723916 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 27723916

Reference Allele: T

Alternative Allele: C

Primary Allele: T

Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGTTGTTTTTTTTTTTTTTATGGAGGGAGTACGTCACATTAAAGTGCCCAACAGCTGCTCAAATGTCCCCGTCGTCTATTCTGAACAGAACTTGTGGAA[T/C]
GGGTGGATGGGCATAAAGACAATGATTTTGACCAAACGCAGAGGGGAAAATATCGGACTTTGGAAGCTGGAAATGATCCCCAACTCTGACCGCTCGGAGA

Reverse complement sequence

TCTCCGAGCGGTCAGAGTTGGGGATCATTTCCAGCTTCCAAAGTCCGATATTTTCCCCTCTGCGTTTGGTCAAAATCATTGTCTTTATGCCCATCCACCC[A/G]
TTCCACAAGTTCTGTTCAGAATAGACGACGGGGACATTTGAGCAGCTGTTGGGCACTTTAATGTGACGTACTCCCTCCATAAAAAAAAAAAAAACAACCT

Allele Frequencies:

Search:

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	70.70%	1.60%	0.40%	27.27%	NA
All Indica	2759	72.20%	1.10%	0.47%	26.24%	NA
All Japonica	1512	76.30%	3.20%	0.26%	20.24%	NA
Aus	269	32.30%	0.00%	0.37%	67.29%	NA
Indica I	595	62.50%	0.50%	0.84%	36.13%	NA
Indica II	465	68.60%	0.00%	0.00%	31.40%	NA
Indica III	913	84.20%	2.10%	0.44%	13.25%	NA
Indica Intermediate	786	67.80%	0.90%	0.51%	30.79%	NA
Temperate Japonica	767	76.40%	6.10%	0.26%	17.21%	NA
Tropical Japonica	504	71.60%	0.20%	0.20%	27.98%	NA
Japonica Intermediate	241	85.90%	0.00%	0.41%	13.69%	NA
VI/Aromatic	96	37.50%	0.00%	0.00%	62.50%	NA
Intermediate	90	78.90%	0.00%	1.11%	20.00%	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
vg1127723916	T -> DEL	N	N	silent_mutation	Average:40.857; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723916	T -> C	LOC_Os11g45820.1	5_prime_UTR_variant ; 328.0bp to feature; MODIFIER	silent_mutation	Average:40.857; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723916	T -> C	LOC_Os11g45809.1	downstream_gene_variant ; 2816.0bp to feature; MODIFIER	silent_mutation	Average:40.857; most accessible tissue: Callus, score: 90.438	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg1127723916:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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