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Detailed information for vg0630422904:

Variant ID: vg0630422904 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 30422904
Reference Allele: CTTGGTCTTGCGAAlternative Allele: C
Primary Allele: CTTGGTCTTGCGASecondary Allele: C

Inferred Ancestral Allele : CTTGGTCTTGCGA (evidence from allele frequency in Oryza rufipogon: CTTGGTCTTGCGA: 0.99, C: 0.02, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AATAGACCAGCTCCTCCTGAGGACGGTAACACCGAAACCCGCTCATGTAGACCGTCTTGAGGTGATCATGGCGGCTCAAGCGATAGTCCTCCCTTGCTAC[CTTGGTCTTGCGA/C]
ACCCGACATTTGTACTTCTTGTAATAATACATCTGCATAATTGTAAACTCTAAGCACAAAAACATGAAAGCTCTAGCTGTTTAATCTATGCATCACACGA

Reverse complement sequence

TCGTGTGATGCATAGATTAAACAGCTAGAGCTTTCATGTTTTTGTGCTTAGAGTTTACAATTATGCAGATGTATTATTACAAGAAGTACAAATGTCGGGT[TCGCAAGACCAAG/G]
GTAGCAAGGGAGGACTATCGCTTGAGCCGCCATGATCACCTCAAGACGGTCTACATGAGCGGGTTTCGGTGTTACCGTCCTCAGGAGGAGCTGGTCTATT

Allele Frequencies:

Populations Population SizeFrequency of CTTGGTCTTGCGA(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.60% 0.40% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 95.20% 4.80% 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 99.80% 0.20% 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  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 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
vg0630422904 CTTGGTCTTGCGA -> C LOC_Os06g50250.1 disruptive_inframe_deletion ; p.Arg56_Lys59del; MODERATE inframe_variant Average:55.223; most accessible tissue: Zhenshan97 root, score: 75.661 N N N N