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Detailed information for vg0125112007:

Variant ID: vg0125112007 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25112007
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGACGTGCGGCGTGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCGGCAGACAACCGAGCTCCCAC[G/A]
TTGCATCTGCTTCCGGCGGAGTGGAGGTAGATATGACCCATCCCATCGGAGGGTCATTCGGACAGCAGCCATTGCAAATCTTCACCCATTAATGAAGGAA

Reverse complement sequence

TTCCTTCATTAATGGGTGAAGATTTGCAATGGCTGCTGTCCGAATGACCCTCCGATGGGATGGGTCATATCTACCTCCACTCCGCCGGAAGCAGATGCAA[C/T]
GTGGGAGCTCGGTTGTCTGCCGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCACGCCGCACGTCT

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 51.00% 0.30% 5.29% 43.42% NA
All Indica  2759 39.80% 0.60% 8.37% 51.29% NA
All Japonica  1512 74.70% 0.00% 0.66% 24.67% NA
Aus  269 16.40% 0.00% 1.12% 82.53% NA
Indica I  595 34.50% 0.00% 14.45% 51.09% NA
Indica II  465 60.20% 0.00% 5.16% 34.62% NA
Indica III  913 30.30% 1.50% 7.34% 60.79% NA
Indica Intermediate  786 42.60% 0.30% 6.87% 50.25% NA
Temperate Japonica  767 98.20% 0.00% 0.13% 1.69% NA
Tropical Japonica  504 44.00% 0.00% 0.99% 54.96% NA
Japonica Intermediate  241 63.90% 0.00% 1.66% 34.44% NA
VI/Aromatic  96 86.50% 0.00% 2.08% 11.46% NA
Intermediate  90 61.10% 0.00% 4.44% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0125112007 G -> A LOC_Os01g43830.1 synonymous_variant ; p.Asn14Asn; LOW synonymous_codon Average:6.081; most accessible tissue: Callus, score: 10.3 N N N N
vg0125112007 G -> DEL LOC_Os01g43830.1 N frameshift_variant Average:6.081; most accessible tissue: Callus, score: 10.3 N N N N