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Detailed information for vg0204059351:

Variant ID: vg0204059351 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4059351
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGATGCAACGCTTTTATTTTGTTAATTACCTCTAGTTGCTCATGTAGCCTTCTTTGCACCTCCATCTGCATTCTGATGGCATCGTTCACGTTGCGGCTG[A/G]
GAGAGAGAATTTCACACACAAGCAAACACAAAAATGGAGTTAGGAAAGAACAAAAAAAAAGAGTAACTGAACAAGGACTAAGAAAGAAATTAAAATCTTA

Reverse complement sequence

TAAGATTTTAATTTCTTTCTTAGTCCTTGTTCAGTTACTCTTTTTTTTTGTTCTTTCCTAACTCCATTTTTGTGTTTGCTTGTGTGTGAAATTCTCTCTC[T/C]
CAGCCGCAACGTGAACGATGCCATCAGAATGCAGATGGAGGTGCAAAGAAGGCTACATGAGCAACTAGAGGTAATTAACAAAATAAAAGCGTTGCATCCA

Allele Frequencies:

Populations Population SizeFrequency of A(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 97.00% 3.00% 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 92.00% 8.00% 0.00% 0.00% NA
Indica III  913 96.10% 3.90% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 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 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
vg0204059351 A -> G LOC_Os02g07770.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:39.75; most accessible tissue: Callus, score: 60.214 N N N N