RiceVarMap2

Detailed information for vg1127723850:

Variant ID: vg1127723850 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 27723850

Reference Allele: T

Alternative Allele: A

Primary Allele: T

Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATTAAAAGTTCGAAGAAAAAGTTTGTAACTAAACTTGGCCTAGGTTGTTTTTTTTGGATGGCGTAGGTTGTTTTTTTTTTTTTTATGGAGGGAGTACG[T/A]
CACATTAAAGTGCCCAACAGCTGCTCAAATGTCCCCGTCGTCTATTCTGAACAGAACTTGTGGAATGGGTGGATGGGCATAAAGACAATGATTTTGACCA

Reverse complement sequence

TGGTCAAAATCATTGTCTTTATGCCCATCCACCCATTCCACAAGTTCTGTTCAGAATAGACGACGGGGACATTTGAGCAGCTGTTGGGCACTTTAATGTG[A/T]
CGTACTCCCTCCATAAAAAAAAAAAAAACAACCTACGCCATCCAAAAAAAACAACCTAGGCCAAGTTTAGTTACAAACTTTTTCTTCGAACTTTTAATTT

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	71.90%	0.50%	0.21%	27.40%	NA
All Indica	2759	72.70%	0.80%	0.25%	26.24%	NA
All Japonica	1512	79.50%	0.10%	0.00%	20.44%	NA
Aus	269	31.20%	0.00%	0.74%	68.03%	NA
Indica I	595	63.00%	0.00%	0.67%	36.30%	NA
Indica II	465	68.60%	0.00%	0.00%	31.40%	NA
Indica III	913	84.10%	2.30%	0.22%	13.36%	NA
Indica Intermediate	786	69.10%	0.30%	0.13%	30.53%	NA
Temperate Japonica	767	82.50%	0.00%	0.00%	17.47%	NA
Tropical Japonica	504	71.80%	0.20%	0.00%	27.98%	NA
Japonica Intermediate	241	85.90%	0.00%	0.00%	14.11%	NA
VI/Aromatic	96	36.50%	0.00%	0.00%	63.54%	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
vg1127723850	T -> A	LOC_Os11g45820.1	5_prime_UTR_variant ; 394.0bp to feature; MODIFIER	silent_mutation	Average:38.42; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723850	T -> A	LOC_Os11g45809.1	downstream_gene_variant ; 2750.0bp to feature; MODIFIER	silent_mutation	Average:38.42; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723850	T -> DEL	N	N	silent_mutation	Average:38.42; 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 vg1127723850:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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