RiceVarMap2

Detailed information for vg0136520925:

Variant ID: vg0136520925 (JBrowse)

Variation Type: SNP

Chromosome: chr01

Position: 36520925

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATATGTATGGAAAGATGAAGTACAAAATACTGCGTAGCAAATTCTACCTATGTGTACCCTCTTAATTAAAAAAAAATCATGTGCACTGAAAGAAAAGT[C/T]
AGTATATGCAAAGTTTAGAGAATATTACTGTATGTAAAAAATCAGCATATACCTCTCTATGTAAAAGTGCAGTATATACTTCTTCGTAACAAGGTCCAGT

Reverse complement sequence

ACTGGACCTTGTTACGAAGAAGTATATACTGCACTTTTACATAGAGAGGTATATGCTGATTTTTTACATACAGTAATATTCTCTAAACTTTGCATATACT[G/A]
ACTTTTCTTTCAGTGCACATGATTTTTTTTTAATTAAGAGGGTACACATAGGTAGAATTTGCTACGCAGTATTTTGTACTTCATCTTTCCATACATATAT

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	35.40%	0.60%	3.49%	60.52%	NA
All Indica	2759	2.90%	0.10%	1.81%	95.22%	NA
All Japonica	1512	95.70%	1.40%	0.26%	2.65%	NA
Aus	269	0.70%	0.00%	40.15%	59.11%	NA
Indica I	595	1.30%	0.00%	1.51%	97.14%	NA
Indica II	465	3.20%	0.00%	1.51%	95.27%	NA
Indica III	913	1.40%	0.00%	1.53%	97.04%	NA
Indica Intermediate	786	5.60%	0.30%	2.54%	91.60%	NA
Temperate Japonica	767	98.80%	0.00%	0.00%	1.17%	NA
Tropical Japonica	504	92.90%	3.40%	0.79%	2.98%	NA
Japonica Intermediate	241	91.70%	1.70%	0.00%	6.64%	NA
VI/Aromatic	96	92.70%	0.00%	1.04%	6.25%	NA
Intermediate	90	63.30%	3.30%	2.22%	31.11%	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
vg0136520925	C -> T	LOC_Os01g63030.1	downstream_gene_variant ; 4312.0bp to feature; MODIFIER	silent_mutation	Average:4.79; most accessible tissue: Callus, score: 8.026	N	N	N	N
vg0136520925	C -> T	LOC_Os01g63040.1	intron_variant ; MODIFIER	silent_mutation	Average:4.79; most accessible tissue: Callus, score: 8.026	N	N	N	N
vg0136520925	C -> DEL	N	N	silent_mutation	Average:4.79; most accessible tissue: Callus, score: 8.026	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg0136520925:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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