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Detailed information for vg0604193490:

Variant ID: vg0604193490 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4193490
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACGTAGCTGATTTGATCTGTCAGATTTAAGCACGAGCCAGATCAAGCATTTTCTGCTGTCGTGAGTAAACATGTCTAGAATTCTACTAGTACTAATTT[T/C]
AAATTTTTAATTAAGTTCATAGAAATATAGAATGCCAGAGAGGAGATTGAGTTGGTAGTGGGAAGAGAGTGGCAGGCAAGCATGCATACACGTTCGGCGA

Reverse complement sequence

TCGCCGAACGTGTATGCATGCTTGCCTGCCACTCTCTTCCCACTACCAACTCAATCTCCTCTCTGGCATTCTATATTTCTATGAACTTAATTAAAAATTT[A/G]
AAATTAGTACTAGTAGAATTCTAGACATGTTTACTCACGACAGCAGAAAATGCTTGATCTGGCTCGTGCTTAAATCTGACAGATCAAATCAGCTACGTCA

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 99.90% 0.10% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0604193490 T -> C LOC_Os06g08490.1 upstream_gene_variant ; 2927.0bp to feature; MODIFIER N Average:56.364; most accessible tissue: Callus, score: 79.267 N N N N
vg0604193490 T -> C LOC_Os06g08500.1 intron_variant ; MODIFIER N Average:56.364; most accessible tissue: Callus, score: 79.267 N N N N