RiceVarMap2

Detailed information for vg1105974506:

Variant ID: vg1105974506 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 5974506

Reference Allele: G

Alternative Allele: C

Primary Allele: G

Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGAC[G/C]
TCTGCCTGCAGCACTAGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATCTGTGCGAGGAGTTGTGCAGCGGTGGAT

Reverse complement sequence

ATCCACCGCTGCACAACTCCTCGCACAGATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCTAGTGCTGCAGGCAGA[C/G]
GTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACC

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	95.70%	0.10%	2.94%	1.21%	NA
All Indica	2759	94.20%	0.20%	4.28%	1.34%	NA
All Japonica	1512	98.40%	0.00%	0.33%	1.26%	NA
Aus	269	94.80%	0.00%	4.83%	0.37%	NA
Indica I	595	93.40%	0.00%	4.71%	1.85%	NA
Indica II	465	92.90%	0.20%	4.30%	2.58%	NA
Indica III	913	94.10%	0.20%	4.82%	0.88%	NA
Indica Intermediate	786	95.70%	0.30%	3.31%	0.76%	NA
Temperate Japonica	767	97.10%	0.00%	0.39%	2.48%	NA
Tropical Japonica	504	99.60%	0.00%	0.40%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	97.80%	0.00%	2.22%	0.00%	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
vg1105974506	G -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:45.682; most accessible tissue: Callus, score: 75.127	N	N	N	N
vg1105974506	G -> C	LOC_Os11g10840.1	missense_variant ; p.Val63Leu; MODERATE	nonsynonymous_codon ; V63L	Average:45.682; most accessible tissue: Callus, score: 75.127	unknown	unknown	TOLERATED	0.30

Showing 1 to 2 of 2 entries

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Detailed information for vg1105974506:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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