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Detailed information for vg0114526919:

Variant ID: vg0114526919 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14526919
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


ATAACAGATCTGCTTGGTTAACTTCCTAAGTATCTGTCTATGTTGCTATGAACAGAACACAATCATGTGCCTTGTGTTCTGGCGAAAAAGGTTACTATCA[T/C]
GTGCGGATTGCATATTTCCAAGTCTTTGGCTTCATTAATTTTGGCCCTGGTCACAGATGATGATGTTGGAAGACATACGTATAAGTTAATGTACCATGAA

Reverse complement sequence

TTCATGGTACATTAACTTATACGTATGTCTTCCAACATCATCATCTGTGACCAGGGCCAAAATTAATGAAGCCAAAGACTTGGAAATATGCAATCCGCAC[A/G]
TGATAGTAACCTTTTTCGCCAGAACACAAGGCACATGATTGTGTTCTGTTCATAGCAACATAGACAGATACTTAGGAAGTTAACCAAGCAGATCTGTTAT

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 95.50% 0.20% 0.68% 3.60% NA
All Indica  2759 93.00% 0.00% 0.94% 6.05% NA
All Japonica  1512 99.40% 0.10% 0.40% 0.07% NA
Aus  269 99.60% 0.00% 0.00% 0.37% NA
Indica I  595 95.30% 0.00% 0.50% 4.20% NA
Indica II  465 97.20% 0.00% 0.22% 2.58% NA
Indica III  913 91.60% 0.00% 1.20% 7.23% NA
Indica Intermediate  786 90.50% 0.00% 1.40% 8.14% NA
Temperate Japonica  767 99.30% 0.00% 0.52% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 0.80% 0.83% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0114526919 T -> DEL N N silent_mutation Average:45.916; most accessible tissue: Zhenshan97 flower, score: 73.683 N N N N
vg0114526919 T -> C LOC_Os01g25630.1 intron_variant ; MODIFIER silent_mutation Average:45.916; most accessible tissue: Zhenshan97 flower, score: 73.683 N N N N