RiceVarMap2

Detailed information for vg1127723898:

Variant ID: vg1127723898 (JBrowse)

Variation Type: INDEL

Chromosome: chr11

Position: 27723898

Reference Allele: TGAACAGAACTTGTGGAATGGGTGGATGGGCATAAAGACAATGATTTTGACCAAACGCAGAGGGGAAAATATCGGACTTTG

Alternative Allele: T

Primary Allele: TGAACAGAACTTGTGGAATG GGTGGATGGGCATAAAGACA ATGATTTTGACCAAACGCAG AGGGGAAAATATCGGACTTT G

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTTTTTTGGATGGCGTAGGTTGTTTTTTTTTTTTTTATGGAGGGAGTACGTCACATTAAAGTGCCCAACAGCTGCTCAAATGTCCCCGTCGTCTATTC[TGAACAGAACTTGTGGAATGGGTGGATGGGCATAAAGACAATGATTTTGACCAAACGCAGAGGGGAAAATATCGGACTTTG/T]
GAAGCTGGAAATGATCCCCAACTCTGACCGCTCGGAGAGCCCGCTCATCCTAACCTGATCTGATGCCTTCAGCTTCTAGGTTCAGTAATCCCTCTCTTCT

Reverse complement sequence

AGAAGAGAGGGATTACTGAACCTAGAAGCTGAAGGCATCAGATCAGGTTAGGATGAGCGGGCTCTCCGAGCGGTCAGAGTTGGGGATCATTTCCAGCTTC[CAAAGTCCGATATTTTCCCCTCTGCGTTTGGTCAAAATCATTGTCTTTATGCCCATCCACCCATTCCACAAGTTCTGTTCA/A]
GAATAGACGACGGGGACATTTGAGCAGCTGTTGGGCACTTTAATGTGACGTACTCCCTCCATAAAAAAAAAAAAAACAACCTACGCCATCCAAAAAAAAC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of TGAACAGAACTTGTGGAATG GGTGGATGGGCATAAAGACA ATGATTTTGACCAAACGCAG AGGGGAAAATATCGGACTTT G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.60%	1.60%	0.44%	27.32%	NA
All Indica	2759	71.00%	2.50%	0.54%	25.95%	NA
All Japonica	1512	78.80%	0.40%	0.40%	20.37%	NA
Aus	269	29.70%	0.40%	0.00%	69.89%	NA
Indica I	595	63.40%	0.20%	0.84%	35.63%	NA
Indica II	465	68.20%	0.00%	0.86%	30.97%	NA
Indica III	913	82.30%	4.30%	0.11%	13.36%	NA
Indica Intermediate	786	65.30%	3.80%	0.64%	30.28%	NA
Temperate Japonica	767	82.00%	0.80%	0.52%	16.69%	NA
Tropical Japonica	504	70.60%	0.00%	0.40%	28.97%	NA
Japonica Intermediate	241	85.90%	0.00%	0.00%	14.11%	NA
VI/Aromatic	96	37.50%	0.00%	0.00%	62.50%	NA
Intermediate	90	78.90%	0.00%	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
vg1127723898	TGAACAGAACTTGTGGAATGGGTGGATGGGCATAAAGACAATGATTTTGACCAAACGCAGAGGGGAAAATATCGGACTTTG -> T	LOC_Os11g45820.1	5_prime_UTR_variant ; 263.0bp to feature; MODIFIER	silent_mutation	Average:40.826; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723898	TGAACAGAACTTGTGGAATGGGTGGATGGGCATAAAGACAATGATTTTGACCAAACGCAGAGGGGAAAATATCGGACTTTG -> T	LOC_Os11g45809.1	downstream_gene_variant ; 2799.0bp to feature; MODIFIER	silent_mutation	Average:40.826; most accessible tissue: Callus, score: 90.438	N	N	N	N
vg1127723898	TGAACAGAACTTGTGGAATGGGTGGATGGGCATAAAGACAATGATTTTGACCAAACGCAGAGGGGAAAATATCGGACTTTG -> DEL	N	N	silent_mutation	Average:40.826; most accessible tissue: Callus, score: 90.438	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg1127723898:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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