RiceVarMap2

Detailed information for vg1127723912:

Variant ID: vg1127723912 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 27723912

Reference Allele: G

Alternative Allele: T

Primary Allele: T

Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGTAGGTTGTTTTTTTTTTTTTTATGGAGGGAGTACGTCACATTAAAGTGCCCAACAGCTGCTCAAATGTCCCCGTCGTCTATTCTGAACAGAACTTGT[G/T]
GAATGGGTGGATGGGCATAAAGACAATGATTTTGACCAAACGCAGAGGGGAAAATATCGGACTTTGGAAGCTGGAAATGATCCCCAACTCTGACCGCTCG

Reverse complement sequence

CGAGCGGTCAGAGTTGGGGATCATTTCCAGCTTCCAAAGTCCGATATTTTCCCCTCTGCGTTTGGTCAAAATCATTGTCTTTATGCCCATCCACCCATTC[C/A]
ACAAGTTCTGTTCAGAATAGACGACGGGGACATTTGAGCAGCTGTTGGGCACTTTAATGTGACGTACTCCCTCCATAAAAAAAAAAAAAACAACCTACGC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.20%	4.10%	0.38%	28.25%	NA
All Indica	2759	69.20%	3.20%	0.51%	27.04%	NA
All Japonica	1512	72.40%	6.50%	0.13%	20.97%	NA
Aus	269	28.30%	0.70%	0.37%	70.63%	NA
Indica I	595	59.20%	1.70%	1.51%	37.65%	NA
Indica II	465	67.10%	0.20%	0.22%	32.47%	NA
Indica III	913	81.90%	4.30%	0.11%	13.69%	NA
Indica Intermediate	786	63.40%	5.00%	0.38%	31.30%	NA
Temperate Japonica	767	69.90%	12.30%	0.13%	17.73%	NA
Tropical Japonica	504	70.60%	0.00%	0.20%	29.17%	NA
Japonica Intermediate	241	83.80%	2.10%	0.00%	14.11%	NA
VI/Aromatic	96	33.30%	0.00%	1.04%	65.62%	NA
Intermediate	90	73.30%	5.60%	0.00%	21.11%	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
vg1127723912	G -> T	LOC_Os11g45820.1	5_prime_UTR_premature_start_codon_gain_variant ; LOW	silent_mutation	Average:41.278; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723912	G -> T	LOC_Os11g45820.1	5_prime_UTR_variant ; 332.0bp to feature; MODIFIER	silent_mutation	Average:41.278; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723912	G -> T	LOC_Os11g45809.1	downstream_gene_variant ; 2812.0bp to feature; MODIFIER	silent_mutation	Average:41.278; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723912	G -> DEL	N	N	silent_mutation	Average:41.278; most accessible tissue: Callus, score: 90.438	N	N	N	N

Showing 1 to 4 of 4 entries

Contact

Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China

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Detailed information for vg1127723912:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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