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Detailed information for vg1123252909:

Variant ID: vg1123252909 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23252909
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATCACAAGATCGATCAGTATCTGCATGTCCACACACATCTCAATATCTCATGGCTACTCGAATTCGAAGGCGCTCCAGTCGATCTTGGCCCATTCTTC[G/C]
TTGATCAGAGCCTCGAGCTTGGCCTGATCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTCGACCTGGCGGCTGACCTCGGCCTGGAACA

Reverse complement sequence

TGTTCCAGGCCGAGGTCAGCCGCCAGGTCGAGGACAACGGCTGCTACGTCGTCGGCGAGAGCTACCTCGCCGATCAGGCCAAGCTCGAGGCTCTGATCAA[C/G]
GAAGAATGGGCCAAGATCGACTGGAGCGCCTTCGAATTCGAGTAGCCATGAGATATTGAGATGTGTGTGGACATGCAGATACTGATCGATCTTGTGATGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.70% 8.30% 0.04% 0.00% NA
All Indica  2759 99.40% 0.50% 0.04% 0.00% NA
All Japonica  1512 75.50% 24.50% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.70% 1.20% 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 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 62.20% 37.70% 0.13% 0.00% NA
Tropical Japonica  504 88.30% 11.70% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1123252909 G -> C LOC_Os11g39060.1 missense_variant ; p.Asn121Lys; MODERATE nonsynonymous_codon Average:65.748; most accessible tissue: Minghui63 root, score: 82.185 unknown unknown TOLERATED 1.00