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Detailed information for vg0629027833:

Variant ID: vg0629027833 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 29027833
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCCGAAGTAGCCGGTGAGCTGGTCGAGGTTGAAGTTGCCATGAGGCAGGTTGACGCTGTTCCTGGTCGACACCCTGCCGTCGAACCTGCCGAGCTCCAC[C/T]
GCGTAGTCCGGTCCTCCACTCTGCATCATGCAGCCAACCCATCAATGGCCATTCGTGCGTGTTCGAATATAAACTAAATTGCCAGTTTTCTCTTATGAGC

Reverse complement sequence

GCTCATAAGAGAAAACTGGCAATTTAGTTTATATTCGAACACGCACGAATGGCCATTGATGGGTTGGCTGCATGATGCAGAGTGGAGGACCGGACTACGC[G/A]
GTGGAGCTCGGCAGGTTCGACGGCAGGGTGTCGACCAGGAACAGCGTCAACCTGCCTCATGGCAACTTCAACCTCGACCAGCTCACCGGCTACTTCGGCA

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 97.60% 1.80% 0.61% 0.00% NA
All Indica  2759 95.90% 3.10% 1.01% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.60% 7.20% 3.19% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 94.30% 4.60% 1.15% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 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
vg0629027833 C -> T LOC_Os06g48010.1 synonymous_variant ; p.Ala143Ala; LOW synonymous_codon Average:73.096; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N