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Detailed information for vg1100142217:

Variant ID: vg1100142217 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 142217
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGGTAGCAAAGTCAGGCATTTACCTAGTCTATGGAAATAAAAGATTGTGATGGACACTATATGCTCTTCAACTGAACTTAATATGGATTGGTTGCATA[C/G]
TGGTTCCTTTTTATGCGGAAGGAACTAACAAATCAACTGATCAATTGGTTGTGATGCCTGCAGGATTCATATTTGCAGTTAACAGGTCCATCTCGTGCAG

Reverse complement sequence

CTGCACGAGATGGACCTGTTAACTGCAAATATGAATCCTGCAGGCATCACAACCAATTGATCAGTTGATTTGTTAGTTCCTTCCGCATAAAAAGGAACCA[G/C]
TATGCAACCAATCCATATTAAGTTCAGTTGAAGAGCATATAGTGTCCATCACAATCTTTTATTTCCATAGACTAGGTAAATGCCTGACTTTGCTACCAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.90% 0.10% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 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  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1100142217 C -> G LOC_Os11g01250.1 upstream_gene_variant ; 1899.0bp to feature; MODIFIER N Average:50.826; most accessible tissue: Callus, score: 78.814 N N N N
vg1100142217 C -> G LOC_Os11g01240.1 downstream_gene_variant ; 3258.0bp to feature; MODIFIER N Average:50.826; most accessible tissue: Callus, score: 78.814 N N N N
vg1100142217 C -> G LOC_Os11g01270.1 downstream_gene_variant ; 1948.0bp to feature; MODIFIER N Average:50.826; most accessible tissue: Callus, score: 78.814 N N N N
vg1100142217 C -> G LOC_Os11g01260.1 intron_variant ; MODIFIER N Average:50.826; most accessible tissue: Callus, score: 78.814 N N N N