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Detailed information for vg0420972175:

Variant ID: vg0420972175 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20972175
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGAGTTTTGCATCCTAGTGAAGTGTGTACAAAGCAAGGAGCATCTCTCTCATACAGTACTGCTCAGCATGCTAGTTCAAGGTGGCTGCTGTAATTTTTG[T/A]
TCTGTCATGTGAGGTTTTATCTTACGTTCATAATGTAAAGTCCCTTTCTGAGATTGGTGAGCTGTGCAATATGTAACTTTCTTGGATTCCATCCATTACA

Reverse complement sequence

TGTAATGGATGGAATCCAAGAAAGTTACATATTGCACAGCTCACCAATCTCAGAAAGGGACTTTACATTATGAACGTAAGATAAAACCTCACATGACAGA[A/T]
CAAAAATTACAGCAGCCACCTTGAACTAGCATGCTGAGCAGTACTGTATGAGAGAGATGCTCCTTGCTTTGTACACACTTCACTAGGATGCAAAACTCTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.70% 0.30% 2.16% 39.86% NA
All Indica  2759 41.20% 0.40% 1.88% 56.47% NA
All Japonica  1512 91.80% 0.00% 1.32% 6.88% NA
Aus  269 27.50% 0.00% 0.74% 71.75% NA
Indica I  595 78.70% 0.00% 1.01% 20.34% NA
Indica II  465 19.10% 0.00% 1.72% 79.14% NA
Indica III  913 35.60% 0.80% 1.64% 61.99% NA
Indica Intermediate  786 32.40% 0.60% 2.93% 63.99% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 78.60% 0.00% 3.97% 17.46% NA
Japonica Intermediate  241 93.80% 0.00% 0.00% 6.22% NA
VI/Aromatic  96 62.50% 0.00% 27.08% 10.42% NA
Intermediate  90 76.70% 0.00% 2.22% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0420972175 T -> DEL N N silent_mutation Average:16.058; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg0420972175 T -> A LOC_Os04g34680.1 downstream_gene_variant ; 4188.0bp to feature; MODIFIER silent_mutation Average:16.058; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg0420972175 T -> A LOC_Os04g34670.1 intron_variant ; MODIFIER silent_mutation Average:16.058; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N