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Detailed information for vg0314254710:

Variant ID: vg0314254710 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14254710
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTCAGAGTCAACAATTACAAGGTACTTCCTTCTTCTTACTACTTTTATTTTCTGATTCAATGCAAGAAAAACTTCATAAGTCTTCAATTTCTCGACCT[C/G]
AATCAATTGTAATCTTGTTGTCCTCTTAAGTTCAACTTGGAACTTTTTGAATATTTTTGAATTGTACAGCTTGACAGCTTGGTACTCAATGTAGTAATGA

Reverse complement sequence

TCATTACTACATTGAGTACCAAGCTGTCAAGCTGTACAATTCAAAAATATTCAAAAAGTTCCAAGTTGAACTTAAGAGGACAACAAGATTACAATTGATT[G/C]
AGGTCGAGAAATTGAAGACTTATGAAGTTTTTCTTGCATTGAATCAGAAAATAAAAGTAGTAAGAAGAAGGAAGTACCTTGTAATTGTTGACTCTGAAAA

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 45.50% 38.20% 13.73% 2.54% NA
All Indica  2759 70.70% 3.20% 21.86% 4.20% NA
All Japonica  1512 0.30% 99.50% 0.20% 0.00% NA
Aus  269 58.40% 29.70% 10.78% 1.12% NA
Indica I  595 62.90% 1.30% 33.11% 2.69% NA
Indica II  465 62.40% 0.90% 29.25% 7.53% NA
Indica III  913 82.90% 4.30% 8.98% 3.83% NA
Indica Intermediate  786 67.40% 4.80% 23.92% 3.82% NA
Temperate Japonica  767 0.00% 99.90% 0.13% 0.00% NA
Tropical Japonica  504 0.60% 99.20% 0.20% 0.00% NA
Japonica Intermediate  241 0.80% 98.80% 0.41% 0.00% NA
VI/Aromatic  96 10.40% 87.50% 2.08% 0.00% NA
Intermediate  90 31.10% 54.40% 13.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0314254710 C -> DEL LOC_Os03g24970.1 N frameshift_variant Average:6.655; most accessible tissue: Callus, score: 16.966 N N N N
vg0314254710 C -> G LOC_Os03g24970.1 missense_variant ; p.Glu59Gln; MODERATE nonsynonymous_codon ; E59Q Average:6.655; most accessible tissue: Callus, score: 16.966 unknown unknown DELETERIOUS 0.01