RiceVarMap2

Detailed information for vg1105974508:

Variant ID: vg1105974508 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 5974508

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGT[C/T]
TGCCTGCAGCACTAGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATCTGTGCGAGGAGTTGTGCAGCGGTGGATTC

Reverse complement sequence

GAATCCACCGCTGCACAACTCCTCGCACAGATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCTAGTGCTGCAGGCA[G/A]
ACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.00%	0.40%	0.63%	48.96%	NA
All Indica	2759	33.20%	0.50%	0.80%	65.57%	NA
All Japonica	1512	83.10%	0.30%	0.40%	16.20%	NA
Aus	269	18.60%	0.00%	0.74%	80.67%	NA
Indica I	595	38.70%	0.30%	2.35%	58.66%	NA
Indica II	465	26.00%	0.00%	0.65%	73.33%	NA
Indica III	913	30.60%	0.20%	0.00%	69.22%	NA
Indica Intermediate	786	36.30%	1.10%	0.64%	61.96%	NA
Temperate Japonica	767	73.10%	0.00%	0.78%	26.08%	NA
Tropical Japonica	504	95.60%	1.00%	0.00%	3.37%	NA
Japonica Intermediate	241	88.40%	0.00%	0.00%	11.62%	NA
VI/Aromatic	96	88.50%	0.00%	0.00%	11.46%	NA
Intermediate	90	63.30%	1.10%	0.00%	35.56%	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
vg1105974508	C -> T	LOC_Os11g10840.1	synonymous_variant ; p.Val63Val; LOW	synonymous_codon	Average:45.682; most accessible tissue: Callus, score: 75.127	N	N	N	N
vg1105974508	C -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:45.682; most accessible tissue: Callus, score: 75.127	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg1105974508:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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