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Detailed information for vg1123253136:

Variant ID: vg1123253136 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23253136
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCAGGGCGGCCATCTTGTCGATCTCCCGGCGCTGCTCCGGCGAGAGGTGCTTCAGGTCGTCGTCGGAGAAGACCGGCCATTGCACCCTCTCGAACGCCA[G/C]
GATGGAGTCGACGTACCCCTGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGGCGGTGGCGGCCGCCGCCGCCGTCGTCTTCTTT

Reverse complement sequence

AAAGAAGACGACGGCGGCGGCGGCCGCCACCGCCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCAGGGGTACGTCGACTCCATC[C/G]
TGGCGTTCGAGAGGGTGCAATGGCCGGTCTTCTCCGACGACGACCTGAAGCACCTCTCGCCGGAGCAGCGCCGGGAGATCGACAAGATGGCCGCCCTGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 6.10% 0.06% 0.00% NA
All Indica  2759 89.60% 10.30% 0.11% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 73.80% 26.00% 0.22% 0.00% NA
Indica Intermediate  786 95.50% 4.50% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 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
vg1123253136 G -> C LOC_Os11g39060.1 missense_variant ; p.Leu46Val; MODERATE nonsynonymous_codon ; L46V Average:67.076; most accessible tissue: Minghui63 root, score: 82.967 unknown unknown DELETERIOUS 0.00