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Detailed information for vg0314254857:

Variant ID: vg0314254857 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14254857
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAATATTTTTGAATTGTACAGCTTGACAGCTTGGTACTCAATGTAGTAATGAGACCAAAGTTTGCTTGGCCTTTTTGTCCTTGAATTATGATCATCTA[A/G]
CTGCTCCAAATTCTGAATAGTGTCCATTACTCTGACATATTCTATCAAAAAGCTTATTATACTGTATTGTGGACCAACATCTTTCTTAAACCTTGAATTT

Reverse complement sequence

AAATTCAAGGTTTAAGAAAGATGTTGGTCCACAATACAGTATAATAAGCTTTTTGATAGAATATGTCAGAGTAATGGACACTATTCAGAATTTGGAGCAG[T/C]
TAGATGATCATAATTCAAGGACAAAAAGGCCAAGCAAACTTTGGTCTCATTACTACATTGAGTACCAAGCTGTCAAGCTGTACAATTCAAAAATATTCAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 19.60% 13.10% 14.98% 52.35% NA
All Indica  2759 0.90% 0.30% 20.70% 78.11% NA
All Japonica  1512 53.20% 39.40% 6.08% 1.26% NA
Aus  269 0.40% 0.00% 10.41% 89.22% NA
Indica I  595 0.00% 0.00% 12.61% 87.39% NA
Indica II  465 0.00% 0.20% 15.91% 83.87% NA
Indica III  913 2.50% 0.10% 32.97% 64.40% NA
Indica Intermediate  786 0.30% 0.80% 15.39% 83.59% NA
Temperate Japonica  767 24.50% 69.00% 6.39% 0.13% NA
Tropical Japonica  504 89.30% 4.40% 3.77% 2.58% NA
Japonica Intermediate  241 69.30% 18.70% 9.96% 2.07% NA
VI/Aromatic  96 71.90% 1.00% 2.08% 25.00% NA
Intermediate  90 30.00% 13.30% 16.67% 40.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0314254857 A -> DEL LOC_Os03g24970.1 N frameshift_variant Average:6.794; most accessible tissue: Callus, score: 16.602 N N N N
vg0314254857 A -> G LOC_Os03g24970.1 synonymous_variant ; p.Leu10Leu; LOW synonymous_codon Average:6.794; most accessible tissue: Callus, score: 16.602 N N N N