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Detailed information for vg0722037209:

Variant ID: vg0722037209 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22037209
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCTCAAATACGTAAATGTCTTTCCCTAATCAAATTCAGGATTTTCTGATTTATGTGCTCTGAAATTGTGAACCACCTGAAGTAGAACTCTTTGTCTGC[G/A]
AAGAAGCTGTGCTATTATGCATCTGCGAAGTTTGACTTGATGAAACATCTGAGAAAAAATTTATGACATCAGGGCTTTCATCAAGAACCTTCAGTGACCT

Reverse complement sequence

AGGTCACTGAAGGTTCTTGATGAAAGCCCTGATGTCATAAATTTTTTCTCAGATGTTTCATCAAGTCAAACTTCGCAGATGCATAATAGCACAGCTTCTT[C/T]
GCAGACAAAGAGTTCTACTTCAGGTGGTTCACAATTTCAGAGCACATAAATCAGAAAATCCTGAATTTGATTAGGGAAAGACATTTACGTATTTGAGAGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.80% 4.20% 0.00% 0.00% NA
All Indica  2759 93.00% 7.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 95.50% 4.50% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 88.60% 11.40% 0.00% 0.00% NA
Indica Intermediate  786 93.50% 6.50% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0722037209 G -> A LOC_Os07g36780.1 missense_variant ; p.Ser809Leu; MODERATE nonsynonymous_codon ; S809L Average:56.366; most accessible tissue: Callus, score: 85.836 unknown unknown TOLERATED 0.07