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Detailed information for vg0101949113:

Variant ID: vg0101949113 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 1949113
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATCTCAATGGCCTTCACCTCAGGCTTCTTGACCTCGGCCTTGGGCACGGTGACAGTGAGCACGCCGTTCTCCAGTCCGGCCTTCACCTGGTCCACCTT[G/C]
GCGTTCTCCGGCAGCCTGAACCGCCGCATGAACTGCCCGCTGCTGCGCTCCACGCGGTGCCACTTGTCGTTCTTGTCCTCCTTCTCCTTGCTGCGCTGGC

Reverse complement sequence

GCCAGCGCAGCAAGGAGAAGGAGGACAAGAACGACAAGTGGCACCGCGTGGAGCGCAGCAGCGGGCAGTTCATGCGGCGGTTCAGGCTGCCGGAGAACGC[C/G]
AAGGTGGACCAGGTGAAGGCCGGACTGGAGAACGGCGTGCTCACTGTCACCGTGCCCAAGGCCGAGGTCAAGAAGCCTGAGGTGAAGGCCATTGAGATCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.40% 5.60% 3.00% 0.00% NA
All Indica  2759 94.90% 0.50% 4.57% 0.00% NA
All Japonica  1512 84.10% 15.00% 0.93% 0.00% NA
Aus  269 93.70% 5.90% 0.37% 0.00% NA
Indica I  595 81.30% 1.30% 17.31% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 0.60% 2.67% 0.00% NA
Temperate Japonica  767 99.00% 0.80% 0.26% 0.00% NA
Tropical Japonica  504 56.70% 41.50% 1.79% 0.00% NA
Japonica Intermediate  241 93.80% 5.00% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 1.11% 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
vg0101949113 G -> C LOC_Os01g04370.1 synonymous_variant ; p.Ala115Ala; LOW synonymous_codon Average:68.604; most accessible tissue: Zhenshan97 flower, score: 87.106 N N N N