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Detailed information for vg1020654113:

Variant ID: vg1020654113 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 20654113
Reference Allele: ACAGAlternative Allele: A
Primary Allele: ACAGSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGGCGAAGTTGTTGGAGGAGACGTTGAAGTAGGTGATGTTGACGAGGGCGAGAAGGCCGAACGGTGCGGCGCCGGAGAAGCTGTTGCTCCCGACGTCGA[ACAG/A]
GTCGAGGCTTCGGCAGCCGTCGAGCTTGCCGTCAATGGCGCCGGAGAGCGAGTTGCTCCGGACAGAAATGTAGCTCATCTCCGGCGGCGCGCACAGTTTA

Reverse complement sequence

TAAACTGTGCGCGCCGCCGGAGATGAGCTACATTTCTGTCCGGAGCAACTCGCTCTCCGGCGCCATTGACGGCAAGCTCGACGGCTGCCGAAGCCTCGAC[CTGT/T]
TCGACGTCGGGAGCAACAGCTTCTCCGGCGCCGCACCGTTCGGCCTTCTCGCCCTCGTCAACATCACCTACTTCAACGTCTCCTCCAACAACTTCGCCGG

Allele Frequencies:

Populations Population SizeFrequency of ACAG(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.10% 0.06% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.30% 0.20% 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  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.00% 0.40% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 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
vg1020654113 ACAG -> A LOC_Os10g38800.1 inframe_deletion ; p.Leu254del; MODERATE N Average:58.742; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N