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Detailed information for vg0807397545:

Variant ID: vg0807397545 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7397545
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:


ACTGGAAGTTCATAAGATTCACGCATGTCCGAACGATTGTATCCTATATCGCGGTGAGGAGTATGAGAACCTAGAAGCATGCCCTGTTTGCAAAGCACTA[C/T]
GATACAAGATTAGACGGGACGATCCAGGAGAAGTTGACGGGCAGCTAACAAAGAAGAGAATTCCTGCTAAGGTGATGTGGTATTTCCCTATAATACCACG

Reverse complement sequence

CGTGGTATTATAGGGAAATACCACATCACCTTAGCAGGAATTCTCTTCTTTGTTAGCTGCCCGTCAACTTCTCCTGGATCGTCCCGTCTAATCTTGTATC[G/A]
TAGTGCTTTGCAAACAGGGCATGCTTCTAGGTTCTCATACTCCTCACCGCGATATAGGATACAATCGTTCGGACATGCGTGAATCTTATGAACTTCCAGT

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 0.20% 0.10% 1.88% 97.82% NA
All Indica  2759 0.30% 0.10% 0.22% 99.35% NA
All Japonica  1512 0.00% 0.10% 5.49% 94.38% NA
Aus  269 0.00% 0.00% 0.00% 100.00% NA
Indica I  595 0.20% 0.20% 0.00% 99.66% NA
Indica II  465 0.20% 0.40% 0.43% 98.92% NA
Indica III  913 0.40% 0.10% 0.33% 99.12% NA
Indica Intermediate  786 0.30% 0.00% 0.13% 99.62% NA
Temperate Japonica  767 0.00% 0.00% 0.13% 99.87% NA
Tropical Japonica  504 0.00% 0.40% 5.16% 94.44% NA
Japonica Intermediate  241 0.00% 0.00% 23.24% 76.76% NA
VI/Aromatic  96 0.00% 0.00% 0.00% 100.00% NA
Intermediate  90 0.00% 0.00% 0.00% 100.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0807397545 C -> T LOC_Os08g12500.1 N stop_gained Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0807397545 C -> DEL LOC_Os08g12500.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N