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Detailed information for vg0137648017:

Variant ID: vg0137648017 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37648017
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGACCCCGTGGCGATCGCCGCGTTCGCCGCCATCGAGCGCGGCATCCTCGTCTCGGCCTCAGCTGGCAACGACGGCCCGAGGCTTGGCACCCTGCACAA[C/T]
GGCATCCCGTGGCTTCTCACCGTCGCCGCCGGCATGGTGGACCGGCAAATGTTCGCCGGATCCATCTACCTCGGCGACGACACGCGGAGCACCATCACCG

Reverse complement sequence

CGGTGATGGTGCTCCGCGTGTCGTCGCCGAGGTAGATGGATCCGGCGAACATTTGCCGGTCCACCATGCCGGCGGCGACGGTGAGAAGCCACGGGATGCC[G/A]
TTGTGCAGGGTGCCAAGCCTCGGGCCGTCGTTGCCAGCTGAGGCCGAGACGAGGATGCCGCGCTCGATGGCGGCGAACGCGGCGATCGCCACGGGGTCTT

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 96.30% 3.40% 0.30% 0.00% NA
All Indica  2759 98.70% 1.30% 0.00% 0.00% NA
All Japonica  1512 91.10% 8.10% 0.73% 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 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.70% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.00% 0.52% 0.00% NA
Tropical Japonica  504 75.40% 23.20% 1.39% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 4.40% 3.33% 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
vg0137648017 C -> T LOC_Os01g64850.1 synonymous_variant ; p.Asn333Asn; LOW synonymous_codon Average:80.823; most accessible tissue: Zhenshan97 flag leaf, score: 86.884 N N N N