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Detailed information for vg1101999370:

Variant ID: vg1101999370 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1999370
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTGCGCTGATTCGCACTGCTTCCATGAGCAGTGCATATTCAGCTGGCTTCTGATTAACCGCCATTGCCCGCTCTGCCGCTTCCCGTTGCCTGCTGAGA[C/G]
GGAGGAGGATGAAGAGGTGGTCCAGGCAGAGAACGACGACGACGACGATGATGAAGAGACCATCCTATGTCTGCATCGACTGTTCGCTGATGCGGCTGAT

Reverse complement sequence

ATCAGCCGCATCAGCGAACAGTCGATGCAGACATAGGATGGTCTCTTCATCATCGTCGTCGTCGTCGTTCTCTGCCTGGACCACCTCTTCATCCTCCTCC[G/C]
TCTCAGCAGGCAACGGGAAGCGGCAGAGCGGGCAATGGCGGTTAATCAGAAGCCAGCTGAATATGCACTGCTCATGGAAGCAGTGCGAATCAGCGCACGG

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 98.20% 1.80% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 87.40% 12.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 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 99.50% 0.50% 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 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 57.30% 42.70% 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
vg1101999370 C -> G LOC_Os11g04690.1 missense_variant ; p.Thr194Arg; MODERATE nonsynonymous_codon ; T194R Average:65.124; most accessible tissue: Minghui63 root, score: 76.425 unknown unknown DELETERIOUS 0.03