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Detailed information for vg1101692944:

Variant ID: vg1101692944 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1692944
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGGACCTCGTCAGGAAGATGCTCAACATCAACCCCAAGGAGAGGCTTACAGCATTCCAAGTGCTCAGTAAGTTTATTTGTTACAGATTAATTACTCAAA[T/C]
CTGCTCCTTTTTTTTTCATATAGAGGTACAGTTTGGATTAATTTTCCCTTTATTGGTGTCAGAATTAAATTTGGATTCATTTGGATCAATTTGGATTTGC

Reverse complement sequence

GCAAATCCAAATTGATCCAAATGAATCCAAATTTAATTCTGACACCAATAAAGGGAAAATTAATCCAAACTGTACCTCTATATGAAAAAAAAAGGAGCAG[A/G]
TTTGAGTAATTAATCTGTAACAAATAAACTTACTGAGCACTTGGAATGCTGTAAGCCTCTCCTTGGGGTTGATGTTGAGCATCTTCCTGACGAGGTCCTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.00% 1.00% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 57.30% 42.70% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1101692944 T -> C LOC_Os11g04150.1 upstream_gene_variant ; 4845.0bp to feature; MODIFIER silent_mutation Average:68.091; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1101692944 T -> C LOC_Os11g04160.1 downstream_gene_variant ; 1604.0bp to feature; MODIFIER silent_mutation Average:68.091; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1101692944 T -> C LOC_Os11g04174.1 downstream_gene_variant ; 1528.0bp to feature; MODIFIER silent_mutation Average:68.091; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1101692944 T -> C LOC_Os11g04180.1 downstream_gene_variant ; 3483.0bp to feature; MODIFIER silent_mutation Average:68.091; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1101692944 T -> C LOC_Os11g04170.1 intron_variant ; MODIFIER silent_mutation Average:68.091; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N