RiceVarMap2

Detailed information for vg1105974391:

Variant ID: vg1105974391 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 5974391

Reference Allele: G

Alternative Allele: C

Primary Allele: G

Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAGCGTGGTGTCGGACCTGAGCCTGCACATGGTGCTGGAGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGG[G/C]
GAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCG

Reverse complement sequence

CGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTC[C/G]
CCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCTCCAGCACCATGTGCAGGCTCAGGTCCGACACCACGCTGT

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	34.80%	21.60%	21.46%	22.11%	NA
All Indica	2759	15.90%	26.70%	30.95%	26.42%	NA
All Japonica	1512	68.90%	14.20%	1.92%	15.01%	NA
Aus	269	16.40%	16.00%	42.38%	25.28%	NA
Indica I	595	35.50%	8.10%	28.74%	27.73%	NA
Indica II	465	15.30%	19.80%	30.11%	34.84%	NA
Indica III	913	2.80%	41.30%	35.93%	19.93%	NA
Indica Intermediate	786	16.50%	28.10%	27.35%	27.99%	NA
Temperate Japonica	767	69.60%	2.90%	2.22%	25.29%	NA
Tropical Japonica	504	64.90%	31.50%	1.98%	1.59%	NA
Japonica Intermediate	241	75.10%	13.70%	0.83%	10.37%	NA
VI/Aromatic	96	88.50%	4.20%	5.21%	2.08%	NA
Intermediate	90	42.20%	23.30%	13.33%	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
vg1105974391	G -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:24.489; most accessible tissue: Callus, score: 34.526	N	N	N	N
vg1105974391	G -> C	LOC_Os11g10840.1	synonymous_variant ; p.Gly24Gly; LOW	synonymous_codon	Average:24.489; most accessible tissue: Callus, score: 34.526	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg1105974391:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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