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Detailed information for vg1124757182:

Variant ID: vg1124757182 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24757182
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


CCGAGCAGCACGATTGCCCTGAGCTCAAGAAGGCCATCCTGAGGTTCATGGCGTCGCCGGCGAGGTTGAAGGCGGTCATGGCGAGCGATGGGTATGAGCA[C/T]
CTGGTGACAAGCTTCCCCTCCATAGCCACGGAGATTCTTGCAATGTTTGCTGCACATTGAGTTCCTAGCTAGCGCATAGAGGATTTTTGGAACGGTAGAG

Reverse complement sequence

CTCTACCGTTCCAAAAATCCTCTATGCGCTAGCTAGGAACTCAATGTGCAGCAAACATTGCAAGAATCTCCGTGGCTATGGAGGGGAAGCTTGTCACCAG[G/A]
TGCTCATACCCATCGCTCGCCATGACCGCCTTCAACCTCGCCGGCGACGCCATGAACCTCAGGATGGCCTTCTTGAGCTCAGGGCAATCGTGCTGCTCGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.50% 4.50% 0.00% 0.00% NA
All Indica  2759 97.70% 2.30% 0.00% 0.00% NA
All Japonica  1512 98.50% 1.50% 0.00% 0.00% NA
Aus  269 54.60% 45.40% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 97.60% 2.40% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1124757182 C -> T LOC_Os11g41300.1 synonymous_variant ; p.His339His; LOW synonymous_codon Average:71.443; most accessible tissue: Callus, score: 82.604 N N N N