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Detailed information for vg1101692021:

Variant ID: vg1101692021 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1692021
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGGCGGGAAGGCCGTCGCCGGCGACGAGGCAGAGCCGGGGACCTCCAAGGCGGCGCCGCCGAGCCGCGGCACCTCCTCCAAAAATGGGTCCGCCAAGCA[G/T]
CAGCCGTGCTCGCCGGCGGCCAAGGCGGCGGCGACGGAAGCGGCGGCGGCGGCGTCGTCGTCCAAGAAGCCGGCAGGCCCCATCGGCGAGGTGCTGGAGC

Reverse complement sequence

GCTCCAGCACCTCGCCGATGGGGCCTGCCGGCTTCTTGGACGACGACGCCGCCGCCGCCGCTTCCGTCGCCGCCGCCTTGGCCGCCGGCGAGCACGGCTG[C/A]
TGCTTGGCGGACCCATTTTTGGAGGAGGTGCCGCGGCTCGGCGGCGCCGCCTTGGAGGTCCCCGGCTCTGCCTCGTCGCCGGCGACGGCCTTCCCGCCAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.20% 0.70% 0.13% 0.00% NA
All Indica  2759 99.60% 0.30% 0.11% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 91.10% 7.80% 1.12% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.13% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 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
vg1101692021 G -> T LOC_Os11g04170.1 missense_variant ; p.Gln40His; MODERATE nonsynonymous_codon ; Q40H Average:62.114; most accessible tissue: Minghui63 panicle, score: 74.563 unknown unknown TOLERATED 0.20