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Detailed information for vg1007670474:

Variant ID: vg1007670474 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7670474
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 395. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCATTCATTACAATAGATAAGTACAAATGCATCAGTCACAAGGTTATGCCTTCGGTATGATCTGAACGAGCATATGCCACAGGCTCTTGGGGATCATC[G/A]
TCAAGGTCAATGTGAGGTCTTACATGAAGATTATGGTTGTATTCTTCTTCATCGACGACGTTGTCAACTCCTACAATTCGGCGCTTTCCATCCCTCACGA

Reverse complement sequence

TCGTGAGGGATGGAAAGCGCCGAATTGTAGGAGTTGACAACGTCGTCGATGAAGAAGAATACAACCATAATCTTCATGTAAGACCTCACATTGACCTTGA[C/T]
GATGATCCCCAAGAGCCTGTGGCATATGCTCGTTCAGATCATACCGAAGGCATAACCTTGTGACTGATGCATTTGTACTTATCTATTGTAATGAATGAAG

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 81.50% 0.00% 0.83% 17.60% NA
All Indica  2759 83.60% 0.10% 0.91% 15.40% NA
All Japonica  1512 74.90% 0.00% 0.73% 24.34% NA
Aus  269 95.50% 0.00% 0.00% 4.46% NA
Indica I  595 76.10% 0.00% 1.51% 22.35% NA
Indica II  465 79.40% 0.20% 1.29% 19.14% NA
Indica III  913 92.90% 0.00% 0.11% 7.01% NA
Indica Intermediate  786 81.00% 0.10% 1.15% 17.68% NA
Temperate Japonica  767 93.50% 0.00% 0.13% 6.39% NA
Tropical Japonica  504 43.10% 0.00% 1.98% 54.96% NA
Japonica Intermediate  241 82.60% 0.00% 0.00% 17.43% NA
VI/Aromatic  96 84.40% 0.00% 1.04% 14.58% NA
Intermediate  90 83.30% 0.00% 2.22% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1007670474 G -> A LOC_Os10g14130.1 synonymous_variant ; p.Asp479Asp; LOW synonymous_codon Average:6.735; most accessible tissue: Callus, score: 17.483 N N N N
vg1007670474 G -> DEL LOC_Os10g14130.1 N frameshift_variant Average:6.735; most accessible tissue: Callus, score: 17.483 N N N N