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Detailed information for vg0627802128:

Variant ID: vg0627802128 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 27802128
Reference Allele: GAlternative Allele: GCCAGGT
Primary Allele: GSecondary Allele: GCCAGGT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCCTCCTCCTGTTTGGCCTGCTGGTCTCGAAGTTTATGCAAGCAATACGAAATGCTACCAAGCTAGCATTTTTGAGGATAACATGTTTTACTATGTGGG[G/GCCAGGT]
CCAGGTAGTTGTACTAGTTAAAATTAGAATCTCTTGAAAATATTAATGGCGAGGGCCATCTCTTTTCCCAAAAGGAAGAGGCCCTCGCGTCGCCCTCCCC

Reverse complement sequence

GGGGAGGGCGACGCGAGGGCCTCTTCCTTTTGGGAAAAGAGATGGCCCTCGCCATTAATATTTTCAAGAGATTCTAATTTTAACTAGTACAACTACCTGG[C/ACCTGGC]
CCCACATAGTAAAACATGTTATCCTCAAAAATGCTAGCTTGGTAGCATTTCGTATTGCTTGCATAAACTTCGAGACCAGCAGGCCAAACAGGAGGAGGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GCCAGGT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 1.10% 0.00% 0.00% NA
All Indica  2759 98.30% 1.70% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 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 95.20% 4.80% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0627802128 G -> GCCAGGT LOC_Os06g45920.1 inframe_insertion ; p.Pro233_Gly234dup; MODERATE inframe_variant Average:70.99; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N