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Detailed information for vg1105342961:

Variant ID: vg1105342961 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5342961
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.63, C: 0.36, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GAGAAAAACACCAATGTTACCATCCTTTAGGTCTCAACCTTCTGAATAATCAAAATGGTGGTGCATCAAGCATCTTCATTGTCATCCTCATTTCCCTCTT[C/G]
GTAAGAGTCTTCGTCTTCATCTTCATCATCATCGTCTTCGTAAGAGTCTTCATCTTCATCTTTATCATCATCGTCTTCGTAAGAGTCTTCATCATCATCT

Reverse complement sequence

AGATGATGATGAAGACTCTTACGAAGACGATGATGATAAAGATGAAGATGAAGACTCTTACGAAGACGATGATGATGAAGATGAAGACGAAGACTCTTAC[G/C]
AAGAGGGAAATGAGGATGACAATGAAGATGCTTGATGCACCACCATTTTGATTATTCAGAAGGTTGAGACCTAAAGGATGGTAACATTGGTGTTTTTCTC

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 82.80% 16.80% 0.36% 0.00% NA
All Indica  2759 93.80% 6.10% 0.11% 0.00% NA
All Japonica  1512 66.40% 33.50% 0.07% 0.00% NA
Aus  269 90.30% 9.70% 0.00% 0.00% NA
Indica I  595 98.30% 1.50% 0.17% 0.00% NA
Indica II  465 95.10% 4.70% 0.22% 0.00% NA
Indica III  913 92.60% 7.40% 0.00% 0.00% NA
Indica Intermediate  786 91.10% 8.80% 0.13% 0.00% NA
Temperate Japonica  767 62.80% 37.20% 0.00% 0.00% NA
Tropical Japonica  504 81.20% 18.70% 0.20% 0.00% NA
Japonica Intermediate  241 46.90% 53.10% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 79.20% 10.42% 0.00% NA
Intermediate  90 76.70% 20.00% 3.33% 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
vg1105342961 C -> G LOC_Os11g09970.1 missense_variant ; p.Glu482Gln; MODERATE nonsynonymous_codon ; E482Q Average:52.154; most accessible tissue: Callus, score: 80.414 unknown unknown TOLERATED 0.27