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Detailed information for vg0204059521:

Variant ID: vg0204059521 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4059521
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.02, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


AACAAGGACTAAGAAAGAAATTAAAATCTTAAACCGGATTAATTCTACAGTACTAGTGTACTGTTACTAGTGTACTAGTGTAGGTGATCTGTGAAAAGAA[C/G]
TTACTCATGGTTCATGCTTCTGCCCATTATGCCTGAAGAAGATGCTGCGTTTCTTTGCATCTCCATTGCCGCGGCTGTGGAAAATTTCAAGAACAAATCA

Reverse complement sequence

TGATTTGTTCTTGAAATTTTCCACAGCCGCGGCAATGGAGATGCAAAGAAACGCAGCATCTTCTTCAGGCATAATGGGCAGAAGCATGAACCATGAGTAA[G/C]
TTCTTTTCACAGATCACCTACACTAGTACACTAGTAACAGTACACTAGTACTGTAGAATTAATCCGGTTTAAGATTTTAATTTCTTTCTTAGTCCTTGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.30% 1.70% 0.00% 0.00% NA
All Indica  2759 98.10% 1.90% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 89.60% 10.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 96.80% 3.20% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% 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  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0204059521 C -> G LOC_Os02g07770.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:41.447; most accessible tissue: Callus, score: 81.19 N N N N