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Detailed information for vg0910657665:

Variant ID: vg0910657665 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10657665
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGAACTTCACCAACGCGGGCCTCCCCAGGACCGCGTTGTAGGGCAGACTGAGGTCCGCCACATCGAAGTCCACCCGCTCCGTGCGGAAGTTGGCGGAA[T/C]
CACCGATGGTGACCGGGAGGTCGATATGACCCAGCGGCCAGGTGTGCCCCGGCGTCACACCGATGATCGGCTGGGACGGCCGGAGCACCATCCCTGGGGC

Reverse complement sequence

GCCCCAGGGATGGTGCTCCGGCCGTCCCAGCCGATCATCGGTGTGACGCCGGGGCACACCTGGCCGCTGGGTCATATCGACCTCCCGGTCACCATCGGTG[A/G]
TTCCGCCAACTTCCGCACGGAGCGGGTGGACTTCGATGTGGCGGACCTCAGTCTGCCCTACAACGCGGTCCTGGGGAGGCCCGCGTTGGTGAAGTTCATG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 38.00% 0.60% 13.46% 47.86% NA
All Indica  2759 29.00% 0.20% 19.83% 50.96% NA
All Japonica  1512 54.80% 1.60% 1.52% 42.13% NA
Aus  269 37.90% 0.00% 21.56% 40.52% NA
Indica I  595 42.50% 0.30% 10.42% 46.72% NA
Indica II  465 22.40% 0.00% 12.90% 64.73% NA
Indica III  913 21.90% 0.10% 32.20% 45.78% NA
Indica Intermediate  786 30.90% 0.40% 16.67% 52.04% NA
Temperate Japonica  767 76.90% 0.10% 0.65% 22.29% NA
Tropical Japonica  504 27.20% 4.60% 2.38% 65.87% NA
Japonica Intermediate  241 41.90% 0.00% 2.49% 55.60% NA
VI/Aromatic  96 32.30% 0.00% 4.17% 63.54% NA
Intermediate  90 41.10% 0.00% 4.44% 54.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0910657665 T -> DEL LOC_Os09g17420.1 N frameshift_variant Average:10.919; most accessible tissue: Callus, score: 20.752 N N N N
vg0910657665 T -> C LOC_Os09g17420.1 missense_variant ; p.Asp69Gly; MODERATE nonsynonymous_codon ; D69G Average:10.919; most accessible tissue: Callus, score: 20.752 benign -0.159 TOLERATED 1.00