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Detailed information for vg0910530241:

Variant ID: vg0910530241 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10530241
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 390. )

Flanking Sequence (100 bp) in Reference Genome:


TATGGTTCAAGTTAAGTTCTCTCTCTCACACACTCATGGCAGTCCTACCAATGGCGACACCGATGTAGGGCACGCTTCTCGGCCCTACCTCAACGGCTGT[C/T]
CCATCGTAGCGCACCTGCCTCACTCAGGGGTGAACCATCTATGCAGGGATACTGCCTCCGCTCGGCTATCTAATCCGCTAGGTCTATACCTATTCGAGAA

Reverse complement sequence

TTCTCGAATAGGTATAGACCTAGCGGATTAGATAGCCGAGCGGAGGCAGTATCCCTGCATAGATGGTTCACCCCTGAGTGAGGCAGGTGCGCTACGATGG[G/A]
ACAGCCGTTGAGGTAGGGCCGAGAAGCGTGCCCTACATCGGTGTCGCCATTGGTAGGACTGCCATGAGTGTGTGAGAGAGAGAACTTAACTTGAACCATA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 22.80% 0.00% 27.74% 49.41% NA
All Indica  2759 18.20% 0.00% 29.68% 52.12% NA
All Japonica  1512 31.00% 0.00% 16.87% 52.18% NA
Aus  269 26.80% 0.40% 56.88% 15.99% NA
Indica I  595 31.90% 0.00% 11.26% 56.81% NA
Indica II  465 12.90% 0.00% 34.41% 52.69% NA
Indica III  913 14.20% 0.00% 38.77% 46.99% NA
Indica Intermediate  786 15.40% 0.10% 30.28% 54.20% NA
Temperate Japonica  767 47.10% 0.00% 4.56% 48.37% NA
Tropical Japonica  504 14.50% 0.00% 36.31% 49.21% NA
Japonica Intermediate  241 14.10% 0.00% 15.35% 70.54% NA
VI/Aromatic  96 6.20% 0.00% 64.58% 29.17% NA
Intermediate  90 34.40% 0.00% 24.44% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0910530241 C -> DEL N N silent_mutation Average:9.669; most accessible tissue: Minghui63 root, score: 15.664 N N N N
vg0910530241 C -> T LOC_Os09g17160.1 intron_variant ; MODIFIER silent_mutation Average:9.669; most accessible tissue: Minghui63 root, score: 15.664 N N N N