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Detailed information for vg0825997781:

Variant ID: vg0825997781 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25997781
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TGTATAAGAAGAAAGTAGCCGTCGGTGACCACTACCTTCTTGAAGTTGCTCTCCGCCATGAAGAAGTCGAGGCACTTGCTCTTCAGCTCCGGGCAGCCGT[G/T]
CATCTCGGCGCAGCCCAGCGTCGTCGCCACCGTCTCCACTGACACGCTCTCCCACAGCTTCTGGGCGCACATCAGCTTCAGCCCGTCCAGCGCGTACCTG

Reverse complement sequence

CAGGTACGCGCTGGACGGGCTGAAGCTGATGTGCGCCCAGAAGCTGTGGGAGAGCGTGTCAGTGGAGACGGTGGCGACGACGCTGGGCTGCGCCGAGATG[C/A]
ACGGCTGCCCGGAGCTGAAGAGCAAGTGCCTCGACTTCTTCATGGCGGAGAGCAACTTCAAGAAGGTAGTGGTCACCGACGGCTACTTTCTTCTTATACA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.30% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0825997781 G -> T LOC_Os08g41150.1 missense_variant ; p.His307Asn; MODERATE nonsynonymous_codon ; H307N Average:68.887; most accessible tissue: Zhenshan97 panicle, score: 85.254 unknown unknown TOLERATED 0.08