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Detailed information for vg0800072268:

Variant ID: vg0800072268 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 72268
Reference Allele: CTCTAlternative Allele: C
Primary Allele: CTCTSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGGGAAGGAATGTTTGTTACTTACATGAAGAGGAAAAAGGCAGTGGGTGGGCGCTTGCCCTTTTTGGCCCCCTCGCCATTGTTGTTGTTGTTCTTGCCG[CTCT/C]
TCTTCTTGCTCGCTGCCACCTCCACGGCCTGCTCCACCACCTGAGCCTCTGTAAGCACAGATCATAGGAAGAAGATGACGATGAGAATCGCAGATTCGTA

Reverse complement sequence

TACGAATCTGCGATTCTCATCGTCATCTTCTTCCTATGATCTGTGCTTACAGAGGCTCAGGTGGTGGAGCAGGCCGTGGAGGTGGCAGCGAGCAAGAAGA[AGAG/G]
CGGCAAGAACAACAACAACAATGGCGAGGGGGCCAAAAAGGGCAAGCGCCCACCCACTGCCTTTTTCCTCTTCATGTAAGTAACAAACATTCCTTCCCTT

Allele Frequencies:

Populations Population SizeFrequency of CTCT(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.30% 4.70% 0.02% 0.00% NA
All Indica  2759 95.40% 4.60% 0.00% 0.00% NA
All Japonica  1512 99.40% 0.50% 0.07% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 89.40% 10.60% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 97.30% 2.70% 0.00% 0.00% NA
Indica Intermediate  786 96.40% 3.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.20% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0800072268 CTCT -> C LOC_Os08g01100.1 disruptive_inframe_deletion ; p.Lys77del; MODERATE inframe_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N