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Detailed information for vg0702317034:

Variant ID: vg0702317034 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 2317034
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TGGAGGCTGGACCTTTTGTGAAGGAGCCCCACATCCAATTTTTTTAAATCAGAATGGGCATCCACATGGTATGAAGAGAAAAGGAACAAAAGGTGTAAGA[A/C]
GAACAATTTTCAGGTAGAGCTCATTACCAGTCAGATTATTTGCACTCAGGTCCAGCTCACTGAGAACCAGAGAATCCCCTTTCAGAAGTCCACTAGGTAC

Reverse complement sequence

GTACCTAGTGGACTTCTGAAAGGGGATTCTCTGGTTCTCAGTGAGCTGGACCTGAGTGCAAATAATCTGACTGGTAATGAGCTCTACCTGAAAATTGTTC[T/G]
TCTTACACCTTTTGTTCCTTTTCTCTTCATACCATGTGGATGCCCATTCTGATTTAAAAAAATTGGATGTGGGGCTCCTTCACAAAAGGTCCAGCCTCCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.40% 0.60% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 90.70% 9.30% 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 99.60% 0.40% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0702317034 A -> C LOC_Os07g05190.1 intron_variant ; MODIFIER silent_mutation Average:42.118; most accessible tissue: Callus, score: 87.473 N N N N