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Detailed information for vg1200762108:

Variant ID: vg1200762108 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 762108
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


GCAACAATGAGATATTTCTCGAGATATGAAACATTTTCCCATAAAATAACTAACTTTCTATATATGTGCATTTTTTTCTTTGGTGCAGGGTCAGTTAAAT[C/A]
AATCCTGCTTGGATCGATCGATCGAGCTTAACATGCTAGCTCAATCGGAGTTGATCAGCTAGTAATTAAGCACGTACTTGCTACAGCATATATGAACAAA

Reverse complement sequence

TTTGTTCATATATGCTGTAGCAAGTACGTGCTTAATTACTAGCTGATCAACTCCGATTGAGCTAGCATGTTAAGCTCGATCGATCGATCCAAGCAGGATT[G/T]
ATTTAACTGACCCTGCACCAAAGAAAAAAATGCACATATATAGAAAGTTAGTTATTTTATGGGAAAATGTTTCATATCTCGAGAAATATCTCATTGTTGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.10% 0.08% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 99.30% 0.50% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 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 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 2.90% 0.83% 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
vg1200762108 C -> A LOC_Os12g02340.2 missense_variant ; p.Gln62Lys; MODERATE nonsynonymous_codon ; Q62K Average:41.081; most accessible tissue: Zhenshan97 flower, score: 80.613 unknown unknown TOLERATED 0.83