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Detailed information for vg1124756897:

Variant ID: vg1124756897 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24756897
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGCGCGGTCGCCGGTGTTCAGGGCGGAGCTCCTCGGCCCCATGAGGGAGCACGCCGCGACGACCATCCGCGTCGACGACATGGACGCCTCCGTGTTCGC[C/A]
GCTCTGCTGCGCTTCGTCTACACCGACGAGCTGCCGGAGCTGGACGGCGGCAGCGCGGCGGCGATGGCGCAGCACCTGCTGGTGGCGGCGGACAGGTACG

Reverse complement sequence

CGTACCTGTCCGCCGCCACCAGCAGGTGCTGCGCCATCGCCGCCGCGCTGCCGCCGTCCAGCTCCGGCAGCTCGTCGGTGTAGACGAAGCGCAGCAGAGC[G/T]
GCGAACACGGAGGCGTCCATGTCGTCGACGCGGATGGTCGTCGCGGCGTGCTCCCTCATGGGGCCGAGGAGCTCCGCCCTGAACACCGGCGACCGCGCCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.10% 0.15% 0.00% NA
All Indica  2759 99.50% 0.30% 0.22% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 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 98.30% 0.90% 0.76% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 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  90 100.00% 0.00% 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
vg1124756897 C -> A LOC_Os11g41300.1 synonymous_variant ; p.Ala244Ala; LOW synonymous_codon Average:73.808; most accessible tissue: Minghui63 flag leaf, score: 84.42 N N N N