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Detailed information for vg0221475862:

Variant ID: vg0221475862 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21475862
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATCTGAACATCACCATAATCAGACCAACAAATCGTCAGCAAGTAAATCCTGCAAAAGGCAAAGCATGCTGTACAGTCTGATACGCGAGAAATCAATCAT[T/C]
CTCTCCCTTACTCTGGAGCATGGTATCCAAATGTTCCTAGCACCCTAGTCGAATGCAACCGGGCAGCGGTGTCGGTGCCCTGGTTCGTCAGGTTGAAATC

Reverse complement sequence

GATTTCAACCTGACGAACCAGGGCACCGACACCGCTGCCCGGTTGCATTCGACTAGGGTGCTAGGAACATTTGGATACCATGCTCCAGAGTAAGGGAGAG[A/G]
ATGATTGATTTCTCGCGTATCAGACTGTACAGCATGCTTTGCCTTTTGCAGGATTTACTTGCTGACGATTTGTTGGTCTGATTATGGTGATGTTCAGATA

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 99.70% 0.30% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 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 98.70% 1.30% 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
vg0221475862 T -> C LOC_Os02g35740.1 upstream_gene_variant ; 4726.0bp to feature; MODIFIER N Average:76.119; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 N N N N
vg0221475862 T -> C LOC_Os02g35750.1 downstream_gene_variant ; 2040.0bp to feature; MODIFIER N Average:76.119; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 N N N N
vg0221475862 T -> C LOC_Os02g35750.2 downstream_gene_variant ; 394.0bp to feature; MODIFIER N Average:76.119; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 N N N N
vg0221475862 T -> C LOC_Os02g35750.3 downstream_gene_variant ; 229.0bp to feature; MODIFIER N Average:76.119; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 N N N N
vg0221475862 T -> C LOC_Os02g35760.1 intron_variant ; MODIFIER N Average:76.119; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 N N N N
vg0221475862 T -> C LOC_Os02g35760.2 intron_variant ; MODIFIER N Average:76.119; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 N N N N