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Detailed information for vg1202830223:

Variant ID: vg1202830223 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2830223
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CTACTCGTGCTTTCTGTGACAAGCCGAACCACAGGATTGTCCACAAGGATAAAAATCTTGTTAGGGTCGAGAGGGATTTGATTGACGTGTTTACACTCCA[T/C]
GAACTTCTGCAGTTATGTGCAAAGAGGAGGTCCCTCTTAGTTGGGAAAAGCTGCCATGGATTAGCCATTCATTTTGGGCTGGTAACTGATACTGTCACAT

Reverse complement sequence

ATGTGACAGTATCAGTTACCAGCCCAAAATGAATGGCTAATCCATGGCAGCTTTTCCCAACTAAGAGGGACCTCCTCTTTGCACATAACTGCAGAAGTTC[A/G]
TGGAGTGTAAACACGTCAATCAAATCCCTCTCGACCCTAACAAGATTTTTATCCTTGTGGACAATCCTGTGGTTCGGCTTGTCACAGAAAGCACGAGTAG

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 99.90% 0.10% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 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 97.80% 2.20% 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
vg1202830223 T -> C LOC_Os12g06070.1 synonymous_variant ; p.His60His; LOW N Average:54.757; most accessible tissue: Callus, score: 79.554 N N N N