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Detailed information for vg0206047442:

Variant ID: vg0206047442 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6047442
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCACGGTGCACACCACCACGACGTACTAGGCTCCTCTCAGCTTGGAGGAGCTCCAGAGGCGCACACTCAGGAGCAGCCAGAGGTCACACCTGTACAGGC[A/T]
GGACGGGTTGGCCGTGCCGTACCCCCGGACCGACTCACGTACTCCCAGGGGCACATTAGGGCGCAGGGTAGGAGGGACAGGGGTAAGAGGCCTCGTCAGT

Reverse complement sequence

ACTGACGAGGCCTCTTACCCCTGTCCCTCCTACCCTGCGCCCTAATGTGCCCCTGGGAGTACGTGAGTCGGTCCGGGGGTACGGCACGGCCAACCCGTCC[T/A]
GCCTGTACAGGTGTGACCTCTGGCTGCTCCTGAGTGTGCGCCTCTGGAGCTCCTCCAAGCTGAGAGGAGCCTAGTACGTCGTGGTGGTGTGCACCGTGCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.70% 13.90% 17.77% 30.60% NA
All Indica  2759 3.20% 23.30% 23.89% 49.58% NA
All Japonica  1512 97.60% 0.20% 1.06% 1.19% NA
Aus  269 50.20% 1.50% 39.03% 9.29% NA
Indica I  595 3.20% 14.50% 33.61% 48.74% NA
Indica II  465 1.50% 37.80% 20.86% 39.78% NA
Indica III  913 2.20% 24.00% 17.31% 56.52% NA
Indica Intermediate  786 5.50% 20.60% 25.95% 47.96% NA
Temperate Japonica  767 98.00% 0.10% 1.30% 0.52% NA
Tropical Japonica  504 97.80% 0.20% 0.40% 1.59% NA
Japonica Intermediate  241 95.40% 0.40% 1.66% 2.49% NA
VI/Aromatic  96 42.70% 0.00% 42.71% 14.58% NA
Intermediate  90 48.90% 6.70% 21.11% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0206047442 A -> T LOC_Os02g11730.1 synonymous_variant ; p.Ala1541Ala; LOW synonymous_codon Average:6.913; most accessible tissue: Minghui63 root, score: 13.235 N N N N
vg0206047442 A -> DEL LOC_Os02g11730.1 N frameshift_variant Average:6.913; most accessible tissue: Minghui63 root, score: 13.235 N N N N