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Detailed information for vg0327370737:

Variant ID: vg0327370737 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27370737
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGTCCGAGCCGTCGGCACGGTCCGCGATGTCGTCGAGCTGGCCGTTGAGGTTCGACCGCGGGATGGGTATAGTGCCGTCGTCATCACCGGCATATAATA[T/C]
ATATTTAAGAAAAGTAAAAATAGGGGGAAACAGTGTGCGCAAGGATATATTCATACACTGACTTGAGAAACATGGCAAGGCTGTGTCCACACGCTGAATT

Reverse complement sequence

AATTCAGCGTGTGGACACAGCCTTGCCATGTTTCTCAAGTCAGTGTATGAATATATCCTTGCGCACACTGTTTCCCCCTATTTTTACTTTTCTTAAATAT[A/G]
TATTATATGCCGGTGATGACGACGGCACTATACCCATCCCGCGGTCGAACCTCAACGGCCAGCTCGACGACATCGCGGACCGTGCCGACGGCTCGGACGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.30% 0.30% 0.32% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 97.90% 1.10% 0.99% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.60% 1.40% 1.96% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 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
vg0327370737 T -> C LOC_Os03g48120.1 missense_variant ; p.Ile19Val; MODERATE N Average:72.076; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0327370737 T -> C LOC_Os03g48140.1 downstream_gene_variant ; 4098.0bp to feature; MODIFIER N Average:72.076; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N