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Detailed information for vg1200762139:

Variant ID: vg1200762139 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 762139
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

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

Flanking Sequence (100 bp) in Reference Genome:


CATTTTCCCATAAAATAACTAACTTTCTATATATGTGCATTTTTTTCTTTGGTGCAGGGTCAGTTAAATCAATCCTGCTTGGATCGATCGATCGAGCTTA[A/G]
CATGCTAGCTCAATCGGAGTTGATCAGCTAGTAATTAAGCACGTACTTGCTACAGCATATATGAACAAAGTAATTAAAATAACAGCTGCGGCAGACATGC

Reverse complement sequence

GCATGTCTGCCGCAGCTGTTATTTTAATTACTTTGTTCATATATGCTGTAGCAAGTACGTGCTTAATTACTAGCTGATCAACTCCGATTGAGCTAGCATG[T/C]
TAAGCTCGATCGATCGATCCAAGCAGGATTGATTTAACTGACCCTGCACCAAAGAAAAAAATGCACATATATAGAAAGTTAGTTATTTTATGGGAAAATG

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 99.90% 0.10% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 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 99.00% 1.00% 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
vg1200762139 A -> G LOC_Os12g02340.2 missense_variant ; p.Asn72Ser; MODERATE nonsynonymous_codon Average:42.623; most accessible tissue: Zhenshan97 flower, score: 80.159 unknown unknown DELETERIOUS 0.01