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Detailed information for vg0114526813:

Variant ID: vg0114526813 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14526813
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


AGATTCACCAAATCGAGAATATGGCATCTCTACCAAATCGACAATATAGCATCTCCAAGGCTTCGAGATAGTACTAGATAATAAATCTGCTTTCCAGGTC[G/A]
TGTTGATAACAGATCTGCTTGGTTAACTTCCTAAGTATCTGTCTATGTTGCTATGAACAGAACACAATCATGTGCCTTGTGTTCTGGCGAAAAAGGTTAC

Reverse complement sequence

GTAACCTTTTTCGCCAGAACACAAGGCACATGATTGTGTTCTGTTCATAGCAACATAGACAGATACTTAGGAAGTTAACCAAGCAGATCTGTTATCAACA[C/T]
GACCTGGAAAGCAGATTTATTATCTAGTACTATCTCGAAGCCTTGGAGATGCTATATTGTCGATTTGGTAGAGATGCCATATTCTCGATTTGGTGAATCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.00% 0.70% 0.40% 3.85% NA
All Indica  2759 91.70% 1.20% 0.65% 6.49% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.07% NA
Aus  269 98.50% 0.70% 0.37% 0.37% NA
Indica I  595 95.00% 0.00% 0.17% 4.87% NA
Indica II  465 94.40% 2.80% 0.00% 2.80% NA
Indica III  913 91.50% 0.10% 0.99% 7.45% NA
Indica Intermediate  786 87.90% 2.30% 1.02% 8.78% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0114526813 G -> A LOC_Os01g25630.1 intron_variant ; MODIFIER silent_mutation Average:51.344; most accessible tissue: Zhenshan97 flower, score: 78.853 N N N N
vg0114526813 G -> DEL N N silent_mutation Average:51.344; most accessible tissue: Zhenshan97 flower, score: 78.853 N N N N