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Detailed information for vg1109584783:

Variant ID: vg1109584783 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9584783
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TGACCCATTCCCCATTAGGACGGTGGAACCCCGTGCGACCTGATAAGAAGAAAACAATGAGATGTCAGCACAAACATGTACATTGGCCCCAGTATCAACC[C/T]
ACCAATTAGTAGATTGATTAACTGAAAAAACAGTAGGTAAATTACCATACCCGCTTCCATCTCCAGTGTTGCCAATGGTCACATTAGCAGACTTAGAAGT

Reverse complement sequence

ACTTCTAAGTCTGCTAATGTGACCATTGGCAACACTGGAGATGGAAGCGGGTATGGTAATTTACCTACTGTTTTTTCAGTTAATCAATCTACTAATTGGT[G/A]
GGTTGATACTGGGGCCAATGTACATGTTTGTGCTGACATCTCATTGTTTTCTTCTTATCAGGTCGCACGGGGTTCCACCGTCCTAATGGGGAATGGGTCA

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 0.60% 0.30% 46.78% 52.35% NA
All Indica  2759 0.40% 0.40% 56.51% 42.73% NA
All Japonica  1512 1.00% 0.00% 20.77% 78.24% NA
Aus  269 0.70% 0.70% 82.16% 16.36% NA
Indica I  595 0.00% 0.50% 24.87% 74.62% NA
Indica II  465 1.10% 0.20% 55.70% 43.01% NA
Indica III  913 0.20% 0.80% 77.22% 21.80% NA
Indica Intermediate  786 0.40% 0.00% 56.87% 42.75% NA
Temperate Japonica  767 0.50% 0.00% 8.34% 91.13% NA
Tropical Japonica  504 1.00% 0.00% 37.70% 61.31% NA
Japonica Intermediate  241 2.50% 0.00% 24.90% 72.61% NA
VI/Aromatic  96 1.00% 0.00% 83.33% 15.62% NA
Intermediate  90 0.00% 0.00% 41.11% 58.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1109584783 C -> T LOC_Os11g17200.1 stop_gained ; p.Trp301*; HIGH stop_gained Average:5.073; most accessible tissue: Zhenshan97 flower, score: 9.663 N N N N
vg1109584783 C -> DEL LOC_Os11g17200.1 N frameshift_variant Average:5.073; most accessible tissue: Zhenshan97 flower, score: 9.663 N N N N