RiceVarMap2

Detailed information for vg0136520805:

Variant ID: vg0136520805 (JBrowse)

Variation Type: SNP

Chromosome: chr01

Position: 36520805

Reference Allele: A

Alternative Allele: T

Primary Allele: A

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACCTTCAAAGCCTGCAGATAATTAGTTTTTCATTTCATAAATAGACAATACTACATGGACCAGTGTATTTAAAATTTCAACATATACTTCTATTTTTT[A/T]
AAAAAAACAGCATACACTCATATATGTATGGAAAGATGAAGTACAAAATACTGCGTAGCAAATTCTACCTATGTGTACCCTCTTAATTAAAAAAAAATCA

Reverse complement sequence

TGATTTTTTTTTAATTAAGAGGGTACACATAGGTAGAATTTGCTACGCAGTATTTTGTACTTCATCTTTCCATACATATATGAGTGTATGCTGTTTTTTT[T/A]
AAAAAATAGAAGTATATGTTGAAATTTTAAATACACTGGTCCATGTAGTATTGTCTATTTATGAAATGAAAAACTAATTATCTGCAGGCTTTGAAGGTTT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.60%	0.10%	16.46%	34.79%	NA
All Indica	2759	19.20%	0.00%	23.92%	56.80%	NA
All Japonica	1512	97.60%	0.20%	0.60%	1.65%	NA
Aus	269	49.40%	0.00%	36.43%	14.13%	NA
Indica I	595	10.80%	0.00%	19.83%	69.41%	NA
Indica II	465	30.10%	0.00%	26.67%	43.23%	NA
Indica III	913	15.20%	0.00%	23.66%	61.12%	NA
Indica Intermediate	786	23.90%	0.10%	25.70%	50.25%	NA
Temperate Japonica	767	99.00%	0.00%	0.13%	0.91%	NA
Tropical Japonica	504	97.40%	0.40%	0.79%	1.39%	NA
Japonica Intermediate	241	93.40%	0.40%	1.66%	4.56%	NA
VI/Aromatic	96	93.80%	1.00%	5.21%	0.00%	NA
Intermediate	90	77.80%	0.00%	6.67%	15.56%	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
vg0136520805	A -> T	LOC_Os01g63030.1	downstream_gene_variant ; 4192.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0136520805	A -> T	LOC_Os01g63040.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0136520805	A -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg0136520805:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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