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Detailed information for vg1013502418:

Variant ID: vg1013502418 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13502418
Reference Allele: CAlternative Allele: T
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: 331. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTCCTCTCAAGATGATATTTTGTCTCCATCAGAGAGAAAAATTCCCGACCTTCTTTCACCAAACCAGCATGACAGCATGCTGAAAGAACACCTATAAA[C/T]
GTAATCTCATCTGGCTTCTGTCCAAGCTCTATCATTGTCCGGAAGTGCTCTATGGCCTCATTGGCATGTCCATGATTTGCTAGACCACATATCATTGCTG

Reverse complement sequence

CAGCAATGATATGTGGTCTAGCAAATCATGGACATGCCAATGAGGCCATAGAGCACTTCCGGACAATGATAGAGCTTGGACAGAAGCCAGATGAGATTAC[G/A]
TTTATAGGTGTTCTTTCAGCATGCTGTCATGCTGGTTTGGTGAAAGAAGGTCGGGAATTTTTCTCTCTGATGGAGACAAAATATCATCTTGAGAGGAAAA

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 93.40% 6.60% 0.00% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 9.70% 90.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg1013502418 C -> T LOC_Os10g26070.1 synonymous_variant ; p.Thr463Thr; LOW synonymous_codon Average:50.88; most accessible tissue: Zhenshan97 young leaf, score: 71.065 N N N N