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Detailed information for vg1200761693:

Variant ID: vg1200761693 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 761693
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATAATTGAATAATTTTTCATAATATACTTGTCTTGGGTTAAAAATGTTACTACTTTTTTTCTACAAAATCAGTCAAACTTATAATAGTTCGACTTTGAC[T/C]
AAAGTCAAAACGTCTTATAACCTGAAACGGAGTAATAGTTAATAAAAACTTTTACAAGTTAAAATAGATTATCATATGTGAGATATATCTCACTTCATAG

Reverse complement sequence

CTATGAAGTGAGATATATCTCACATATGATAATCTATTTTAACTTGTAAAAGTTTTTATTAACTATTACTCCGTTTCAGGTTATAAGACGTTTTGACTTT[A/G]
GTCAAAGTCGAACTATTATAAGTTTGACTGATTTTGTAGAAAAAAAGTAGTAACATTTTTAACCCAAGACAAGTATATTATGAAAAATTATTCAATTATA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.20% 0.02% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 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 99.80% 0.20% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg1200761693 T -> C LOC_Os12g02350.1 upstream_gene_variant ; 2098.0bp to feature; MODIFIER N Average:32.028; most accessible tissue: Zhenshan97 flower, score: 75.428 N N N N
vg1200761693 T -> C LOC_Os12g02370.2 downstream_gene_variant ; 4741.0bp to feature; MODIFIER N Average:32.028; most accessible tissue: Zhenshan97 flower, score: 75.428 N N N N
vg1200761693 T -> C LOC_Os12g02370.4 downstream_gene_variant ; 4741.0bp to feature; MODIFIER N Average:32.028; most accessible tissue: Zhenshan97 flower, score: 75.428 N N N N
vg1200761693 T -> C LOC_Os12g02340.1 intron_variant ; MODIFIER N Average:32.028; most accessible tissue: Zhenshan97 flower, score: 75.428 N N N N
vg1200761693 T -> C LOC_Os12g02340.2 intron_variant ; MODIFIER N Average:32.028; most accessible tissue: Zhenshan97 flower, score: 75.428 N N N N