RiceVarMap2

Detailed information for vg1127723838:

Variant ID: vg1127723838 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 27723838

Reference Allele: G

Alternative Allele: C

Primary Allele: G

Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATGTGATAGAAAAATTAAAAGTTCGAAGAAAAAGTTTGTAACTAAACTTGGCCTAGGTTGTTTTTTTTGGATGGCGTAGGTTGTTTTTTTTTTTTTTAT[G/C]
GAGGGAGTACGTCACATTAAAGTGCCCAACAGCTGCTCAAATGTCCCCGTCGTCTATTCTGAACAGAACTTGTGGAATGGGTGGATGGGCATAAAGACAA

Reverse complement sequence

TTGTCTTTATGCCCATCCACCCATTCCACAAGTTCTGTTCAGAATAGACGACGGGGACATTTGAGCAGCTGTTGGGCACTTTAATGTGACGTACTCCCTC[C/G]
ATAAAAAAAAAAAAAACAACCTACGCCATCCAAAAAAAACAACCTAGGCCAAGTTTAGTTACAAACTTTTTCTTCGAACTTTTAATTTTTCTATCACATC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.60%	0.70%	0.25%	27.44%	NA
All Indica	2759	72.60%	0.90%	0.33%	26.24%	NA
All Japonica	1512	79.00%	0.50%	0.00%	20.50%	NA
Aus	269	30.90%	0.00%	0.74%	68.40%	NA
Indica I	595	62.70%	0.20%	0.67%	36.47%	NA
Indica II	465	66.70%	1.90%	0.00%	31.40%	NA
Indica III	913	86.20%	0.20%	0.33%	13.25%	NA
Indica Intermediate	786	67.70%	1.50%	0.25%	30.53%	NA
Temperate Japonica	767	82.10%	0.30%	0.00%	17.60%	NA
Tropical Japonica	504	70.80%	1.20%	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
vg1127723838	G -> DEL	N	N	silent_mutation	Average:37.806; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723838	G -> C	LOC_Os11g45820.1	5_prime_UTR_variant ; 406.0bp to feature; MODIFIER	silent_mutation	Average:37.806; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723838	G -> C	LOC_Os11g45809.1	downstream_gene_variant ; 2738.0bp to feature; MODIFIER	silent_mutation	Average:37.806; 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 vg1127723838:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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