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Detailed information for vg0302879570:

Variant ID: vg0302879570 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 2879570
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGCGCAGTTCTCCGAGAAGGGGTTCAGCGCCGACGAGATGGTCGTCCTCCTCGCCGGCGGCCACTCCATCGGCAAGGCCAAGTGCTTCTTCATCGAGGT[C/T]
GACGCGGCGCCCATCGACCCGACCTACCGCTCCAACATCACCGCCTTCTGCGACGGCAAGGACGGCGACAAGGGAGCCGTCCCCCTTGATCCCATCACCC

Reverse complement sequence

GGGTGATGGGATCAAGGGGGACGGCTCCCTTGTCGCCGTCCTTGCCGTCGCAGAAGGCGGTGATGTTGGAGCGGTAGGTCGGGTCGATGGGCGCCGCGTC[G/A]
ACCTCGATGAAGAAGCACTTGGCCTTGCCGATGGAGTGGCCGCCGGCGAGGAGGACGACCATCTCGTCGGCGCTGAACCCCTTCTCGGAGAACTGCGCCA

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 99.80% 0.10% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 97.00% 2.20% 0.74% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 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
vg0302879570 C -> T LOC_Os03g05770.1 synonymous_variant ; p.Val205Val; LOW synonymous_codon Average:77.349; most accessible tissue: Zhenshan97 young leaf, score: 85.184 N N N N