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Detailed information for vg0221169385:

Variant ID: vg0221169385 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21169385
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGGTCCATATACATTCAAGGTTACAACAGTTCTCTGCAAGATTTCTCACTGGATTTATGGTGTCCTCCTCCATCTCTCCTGCAAAAATTTGTTGCCAA[T/C]
AAGTGTCTCAGTGTGATTCCAAACTGGTTGGGCTCACTTATCAACCTATCTTACATCAACGTCGATGTTCTTCGAGCGGCACAAAGAGATCTGGATATCC

Reverse complement sequence

GGATATCCAGATCTCTTTGTGCCGCTCGAAGAACATCGACGTTGATGTAAGATAGGTTGATAAGTGAGCCCAACCAGTTTGGAATCACACTGAGACACTT[A/G]
TTGGCAACAAATTTTTGCAGGAGAGATGGAGGAGGACACCATAAATCCAGTGAGAAATCTTGCAGAGAACTGTTGTAACCTTGAATGTATATGGACCGGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.30% 33.60% 0.11% 0.00% NA
All Indica  2759 99.00% 0.80% 0.14% 0.00% NA
All Japonica  1512 2.00% 98.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.50% 0.17% 0.00% NA
Indica II  465 98.70% 1.10% 0.22% 0.00% NA
Indica III  913 99.20% 0.70% 0.11% 0.00% NA
Indica Intermediate  786 98.70% 1.10% 0.13% 0.00% NA
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 1.80% 98.20% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 56.20% 42.70% 1.04% 0.00% NA
Intermediate  90 54.40% 45.60% 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
vg0221169385 T -> C LOC_Os02g35210.1 synonymous_variant ; p.Asn759Asn; LOW synonymous_codon Average:64.926; most accessible tissue: Minghui63 flag leaf, score: 80.786 N N N N