RiceVarMap2

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Detailed information for vg1127724099:

Variant ID: vg1127724099 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 27724099
Reference Allele: A	Alternative Allele: AGAGAGAATCCACTCAG,AGAGAGAATCCACTCAGTACCAC,AGAGAGAATCCACTCAGTACCACTGAGTT,AGAGAGAATCCACTCAGTACCACTGAGTTTTCCCCACT,AGAGAGAATCCACTCAGTACCACTGAGTTTTCCCCAC,AGAGAGAATCCACTCAGTACCACTGAGTTT
Primary Allele: A	Secondary Allele: AGAGAGAATCCACTCAGTAC CAC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCTGACCGCTCGGAGAGCCCGCTCATCCTAACCTGATCTGATGCCTTCAGCTTCTAGGTTCAGTAATCCCTCTCTTCTTCGCTTCAGTGATTTATCTA[A/AGAGAGAATCCACTCAG,AGAGAGAATCCACTCAGTACCAC,AGAGAGAATCCACTCAGTACCACTGAGTT,AGAGAGAATCCACTCAGTACCACTGAGTTTTCCCCACT,AGAGAGAATCCACTCAGTACCACTGAGTTTTCCCCAC,AGAGAGAATCCACTCAGTACCACTGAGTTT]
TGCCTTCAACTGCTATTCAGTAATCCCTCTCTAGCTTTGTTTGCTTCAGTGATTTCAATTTTATTATTTGCTTCTGTTCAGCAGTACGTATGCCTTGCAA

Reverse complement sequence

TTGCAAGGCATACGTACTGCTGAACAGAAGCAAATAATAAAATTGAAATCACTGAAGCAAACAAAGCTAGAGAGGGATTACTGAATAGCAGTTGAAGGCA[T/CTGAGTGGATTCTCTCT,GTGGTACTGAGTGGATTCTCTCT,AACTCAGTGGTACTGAGTGGATTCTCTCT,AGTGGGGAAAACTCAGTGGTACTGAGTGGATTCTCTCT,GTGGGGAAAACTCAGTGGTACTGAGTGGATTCTCTCT,AAACTCAGTGGTACTGAGTGGATTCTCTCT]
TAGATAAATCACTGAAGCGAAGAAGAGAGGGATTACTGAACCTAGAAGCTGAAGGCATCAGATCAGGTTAGGATGAGCGGGCTCTCCGAGCGGTCAGAGT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of AGAGAGAATCCACTCAGTAC CAC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.40%	0.10%	0.87%	27.42%	AGAGAGAATCCACTCAGTACCACTGAGTTTTCCCCAC: 0.06%; AGAGAGAATCCACTCAG: 0.04%; AGAGAGAATCCACTCAGTACCACTGAGTTT: 0.02%
All Indica	2759	72.10%	0.20%	1.12%	26.35%	AGAGAGAATCCACTCAGTACCACTGAGTTTTCCCCAC: 0.11%; AGAGAGAATCCACTCAG: 0.07%; AGAGAGAATCCACTCAGTACCACTGAGTTT: 0.04%
All Japonica	1512	79.20%	0.10%	0.40%	20.30%	NA
Aus	269	31.20%	0.00%	0.74%	68.03%	NA
Indica I	595	62.90%	0.00%	1.68%	35.29%	AGAGAGAATCCACTCAG: 0.17%
Indica II	465	68.20%	0.00%	0.22%	31.61%	NA
Indica III	913	84.40%	0.30%	1.20%	13.80%	AGAGAGAATCCACTCAGTACCACTGAGTTT: 0.11%; AGAGAGAATCCACTCAGTACCACTGAGTTTTCCCCAC: 0.11%
Indica Intermediate	786	67.00%	0.40%	1.15%	31.04%	AGAGAGAATCCACTCAGTACCACTGAGTTTTCCCCAC: 0.25%; AGAGAGAATCCACTCAG: 0.13%
Temperate Japonica	767	82.50%	0.00%	0.26%	17.21%	NA
Tropical Japonica	504	70.80%	0.20%	0.60%	28.37%	NA
Japonica Intermediate	241	86.30%	0.00%	0.41%	13.28%	NA
VI/Aromatic	96	35.40%	0.00%	1.04%	63.54%	NA
Intermediate	90	78.90%	0.00%	1.11%	20.00%	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
vg1127724099	A -> AGAGAGAATCCACTCAGTACCACTGAGTTT TCCCCAC	LOC_Os11g45820.1	5_prime_UTR_variant ; 144.0bp to feature; MODIFIER	silent_mutation	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAGTACCACTGAGTTT TCCCCAC	LOC_Os11g45809.1	downstream_gene_variant ; 3000.0bp to feature; MODIFIER	silent_mutation	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAGTACCACTGAGTT	LOC_Os11g45820.1	5_prime_UTR_variant ; 144.0bp to feature; MODIFIER	N	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAGTACCACTGAGTT	LOC_Os11g45809.1	downstream_gene_variant ; 3000.0bp to feature; MODIFIER	N	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAGTACCACTGAGTTT	LOC_Os11g45820.1	5_prime_UTR_variant ; 144.0bp to feature; MODIFIER	silent_mutation	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAGTACCACTGAGTTT	LOC_Os11g45809.1	downstream_gene_variant ; 3000.0bp to feature; MODIFIER	silent_mutation	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAG	LOC_Os11g45820.1	5_prime_UTR_variant ; 144.0bp to feature; MODIFIER	silent_mutation	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAG	LOC_Os11g45809.1	downstream_gene_variant ; 3000.0bp to feature; MODIFIER	silent_mutation	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> DEL	N	N	silent_mutation	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAGTACCACTGAGTTT TCCCCACT	LOC_Os11g45820.1	5_prime_UTR_variant ; 144.0bp to feature; MODIFIER	N	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAGTACCACTGAGTTT TCCCCACT	LOC_Os11g45809.1	downstream_gene_variant ; 3000.0bp to feature; MODIFIER	N	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAGTACCAC	LOC_Os11g45820.1	5_prime_UTR_variant ; 144.0bp to feature; MODIFIER	silent_mutation	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724099	A -> AGAGAGAATCCACTCAGTACCAC	LOC_Os11g45809.1	downstream_gene_variant ; 3000.0bp to feature; MODIFIER	silent_mutation	Average:51.342; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N

Showing 1 to 13 of 13 entries

Search for Variation information by Variation ID:

Detailed information for vg1127724099:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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