RiceVarMap2

Detailed information for vg1105974430:

Variant ID: vg1105974430 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 5974430

Reference Allele: T

Alternative Allele: C

Primary Allele: T

Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTT[T/C]
CGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCA

Reverse complement sequence

TGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCG[A/G]
AACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCT

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	46.50%	0.20%	3.39%	49.94%	NA
All Indica	2759	32.50%	0.40%	1.78%	65.31%	NA
All Japonica	1512	74.50%	0.00%	6.02%	19.44%	NA
Aus	269	18.20%	0.00%	2.97%	78.81%	NA
Indica I	595	37.60%	0.30%	2.69%	59.33%	NA
Indica II	465	22.80%	0.60%	2.58%	73.98%	NA
Indica III	913	30.80%	0.40%	0.88%	67.91%	NA
Indica Intermediate	786	36.50%	0.10%	1.65%	61.70%	NA
Temperate Japonica	767	65.80%	0.00%	6.00%	28.16%	NA
Tropical Japonica	504	85.50%	0.00%	5.95%	8.53%	NA
Japonica Intermediate	241	79.30%	0.00%	6.22%	14.52%	NA
VI/Aromatic	96	69.80%	0.00%	9.38%	20.83%	NA
Intermediate	90	61.10%	0.00%	3.33%	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
vg1105974430	T -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:33.674; most accessible tissue: Callus, score: 75.127	N	N	N	N
vg1105974430	T -> C	LOC_Os11g10840.1	synonymous_variant ; p.Phe37Phe; LOW	synonymous_codon	Average:33.674; 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 vg1105974430:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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