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Detailed information for vg0704649907:

Variant ID: vg0704649907 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4649907
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.03, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


AACCATGGATCATGCCATGGTAAAGGACGATAACCTAAGGTCATCTCAGCTTTGTACCATGGAATTGCCGCTCTCCAAGGTGATACTGGTGGAGAGCTAC[C/A]
TGTTTGCAGTAGTGTGAACTTGGAATTCACTTTAGTGAGCTCAACTAAATCCTCGGTGGCCATGTCATCGTCATCATCATTGATCATTTGTTCATTGCCT

Reverse complement sequence

AGGCAATGAACAAATGATCAATGATGATGACGATGACATGGCCACCGAGGATTTAGTTGAGCTCACTAAAGTGAATTCCAAGTTCACACTACTGCAAACA[G/T]
GTAGCTCTCCACCAGTATCACCTTGGAGAGCGGCAATTCCATGGTACAAAGCTGAGATGACCTTAGGTTATCGTCCTTTACCATGGCATGATCCATGGTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.70% 40.90% 0.08% 0.23% NA
All Indica  2759 97.40% 2.20% 0.07% 0.36% NA
All Japonica  1512 0.30% 99.50% 0.07% 0.07% NA
Aus  269 18.60% 81.40% 0.00% 0.00% NA
Indica I  595 99.30% 0.30% 0.00% 0.34% NA
Indica II  465 97.00% 2.80% 0.22% 0.00% NA
Indica III  913 98.10% 1.40% 0.00% 0.44% NA
Indica Intermediate  786 95.30% 4.10% 0.13% 0.51% NA
Temperate Japonica  767 0.30% 99.60% 0.13% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.20% 0.00% 0.41% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 36.70% 62.20% 1.11% 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
vg0704649907 C -> DEL LOC_Os07g08940.1 N frameshift_variant Average:42.577; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N
vg0704649907 C -> A LOC_Os07g08940.1 missense_variant ; p.Gly217Cys; MODERATE nonsynonymous_codon ; G217C Average:42.577; most accessible tissue: Zhenshan97 young leaf, score: 70.625 unknown unknown TOLERATED 0.06