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Detailed information for vg0910530299:

Variant ID: vg0910530299 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10530299
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: 318. )

Flanking Sequence (100 bp) in Reference Genome:


ACCGATGTAGGGCACGCTTCTCGGCCCTACCTCAACGGCTGTCCCATCGTAGCGCACCTGCCTCACTCAGGGGTGAACCATCTATGCAGGGATACTGCCT[C/T]
CGCTCGGCTATCTAATCCGCTAGGTCTATACCTATTCGAGAAGTACGGTTGTACGGGGGTCGTTTCATGCTTAACTTCATGGCCCAGTCCTTAATTGACC

Reverse complement sequence

GGTCAATTAAGGACTGGGCCATGAAGTTAAGCATGAAACGACCCCCGTACAACCGTACTTCTCGAATAGGTATAGACCTAGCGGATTAGATAGCCGAGCG[G/A]
AGGCAGTATCCCTGCATAGATGGTTCACCCCTGAGTGAGGCAGGTGCGCTACGATGGGACAGCCGTTGAGGTAGGGCCGAGAAGCGTGCCCTACATCGGT

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 11.30% 0.10% 23.91% 64.68% NA
All Indica  2759 4.00% 0.20% 23.05% 72.71% NA
All Japonica  1512 25.90% 0.00% 21.83% 52.31% NA
Aus  269 5.60% 0.40% 29.00% 65.06% NA
Indica I  595 6.60% 0.30% 26.55% 66.55% NA
Indica II  465 0.60% 0.00% 24.52% 74.84% NA
Indica III  913 4.90% 0.30% 20.70% 74.04% NA
Indica Intermediate  786 3.10% 0.10% 22.26% 74.55% NA
Temperate Japonica  767 46.40% 0.00% 7.82% 45.76% NA
Tropical Japonica  504 2.20% 0.00% 43.65% 54.17% NA
Japonica Intermediate  241 10.00% 0.00% 20.75% 69.29% NA
VI/Aromatic  96 2.10% 0.00% 52.08% 45.83% NA
Intermediate  90 14.40% 0.00% 40.00% 45.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0910530299 C -> DEL N N silent_mutation Average:9.393; most accessible tissue: Minghui63 root, score: 13.235 N N N N
vg0910530299 C -> T LOC_Os09g17160.1 intron_variant ; MODIFIER silent_mutation Average:9.393; most accessible tissue: Minghui63 root, score: 13.235 N N N N