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Detailed information for vg0710993130:

Variant ID: vg0710993130 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 10993130
Reference Allele: AAlternative Allele: AAT
Primary Allele: ASecondary Allele: AAT

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


TGTATTCTTCCCATAGTTGATTCCTTTAAATCAAAAAACAAGGAAGAATTTTCACCATGATGTACAGCTTCTCCAAGCATGGAAAACATTTAAGGAAGCC[A/AAT]
AATTGTGTCCAGATTTGGTCCAGCAGACTCAAGAACCAAAACCTTCACTGTGCGCAGCGAGGCTGTCGAACTGACGACCATCGTTTCCTGAAGAAAACCA

Reverse complement sequence

TGGTTTTCTTCAGGAAACGATGGTCGTCAGTTCGACAGCCTCGCTGCGCACAGTGAAGGTTTTGGTTCTTGAGTCTGCTGGACCAAATCTGGACACAATT[T/ATT]
GGCTTCCTTAAATGTTTTCCATGCTTGGAGAAGCTGTACATCATGGTGAAAATTCTTCCTTGTTTTTTGATTTAAAGGAATCAACTATGGGAAGAATACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of AAT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.50% 9.50% 0.02% 0.00% NA
All Indica  2759 97.80% 2.10% 0.04% 0.00% NA
All Japonica  1512 80.40% 19.60% 0.00% 0.00% NA
Aus  269 95.20% 4.80% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 92.60% 7.30% 0.13% 0.00% NA
Temperate Japonica  767 66.90% 33.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 83.80% 16.20% 0.00% 0.00% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0710993130 A -> AAT LOC_Os07g18600.1 frameshift_variant ; p.Trp338fs; HIGH frameshift_variant Average:40.102; most accessible tissue: Callus, score: 67.589 N N N N