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Detailed information for vg0905621406:

Variant ID: vg0905621406 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5621406
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CTGCCTCCTGACAAGCATGAATATAATCTCTTCCTCCAGCTTCAAACATCATTGATGGAAGGTCTTCACGATCACTAGTCAACGTCATGCGAACACGACT[A/G]
TTCTCCTCATTGGGGTCATGGGGAATTTGGCGATACTCGGGGACAATGTTGTAGCCTACTTCAAATGCCATCATTCTCAGCTCCCTGACGAATCCTACTG

Reverse complement sequence

CAGTAGGATTCGTCAGGGAGCTGAGAATGATGGCATTTGAAGTAGGCTACAACATTGTCCCCGAGTATCGCCAAATTCCCCATGACCCCAATGAGGAGAA[T/C]
AGTCGTGTTCGCATGACGTTGACTAGTGATCGTGAAGACCTTCCATCAATGATGTTTGAAGCTGGAGGAAGAGATTATATTCATGCTTGTCAGGAGGCAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.70% 2.30% 0.00% 0.00% NA
All Indica  2759 97.40% 2.60% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 87.40% 12.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 93.50% 6.50% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 95.40% 4.60% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0905621406 A -> G LOC_Os09g10310.1 synonymous_variant ; p.Asn41Asn; LOW synonymous_codon Average:41.722; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N