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Detailed information for vg1212722969:

Variant ID: vg1212722969 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 12722969
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGACATGATGTTGAGGCTGTGTCTTGTGTGTACAGTGGTACACCTCTGGCCAGAGTAAAACTATTCGAATAGCCGTGCCCACGGTTATGGGCGGGTTGAG[T/C]
AATGTTTTTCGTGATTAGTCTCACACCTCTCACAACAATTATTGATGCTATAACTGGTAATAATTTGCTTAGCTCCTGGTTTGGAGTTAGATCTGTACAG

Reverse complement sequence

CTGTACAGATCTAACTCCAAACCAGGAGCTAAGCAAATTATTACCAGTTATAGCATCAATAATTGTTGTGAGAGGTGTGAGACTAATCACGAAAAACATT[A/G]
CTCAACCCGCCCATAACCGTGGGCACGGCTATTCGAATAGTTTTACTCTGGCCAGAGGTGTACCACTGTACACACAAGACACAGCCTCAACATCATGTCT

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 99.70% 0.10% 0.13% 0.00% NA
All Indica  2759 99.80% 0.10% 0.11% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 98.90% 0.70% 0.37% 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 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.50% 0.30% 0.25% 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 96.70% 1.10% 2.22% 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
vg1212722969 T -> C LOC_Os12g22540.1 synonymous_variant ; p.Ser74Ser; LOW synonymous_codon Average:57.292; most accessible tissue: Zhenshan97 flag leaf, score: 77.473 N N N N