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Detailed information for vg0605310329:

Variant ID: vg0605310329 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5310329
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


ATGAGTTGATAATCGACCTATACAATGTAAGCTTTGATGTCCGTGCTATCCGTTCTTACATATCAATGTACTGCCAAATAACCTTCAGCAGAGTGCATTA[T/C]
CATTTTTTTAAGAGAACTTCAAAACCATTTTGACATCAAGGCTTGAAAGTTAATTGTAGGTGTAGCATACTGACTTGGTTTCTAAACTAATTACTGATGA

Reverse complement sequence

TCATCAGTAATTAGTTTAGAAACCAAGTCAGTATGCTACACCTACAATTAACTTTCAAGCCTTGATGTCAAAATGGTTTTGAAGTTCTCTTAAAAAAATG[A/G]
TAATGCACTCTGCTGAAGGTTATTTGGCAGTACATTGATATGTAAGAACGGATAGCACGGACATCAAAGCTTACATTGTATAGGTCGATTATCAACTCAT

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 99.20% 0.60% 0.17% 0.00% NA
All Indica  2759 98.90% 0.80% 0.29% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 97.50% 2.50% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.00% 0.51% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 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
vg0605310329 T -> C LOC_Os06g10350.1 upstream_gene_variant ; 4849.0bp to feature; MODIFIER silent_mutation Average:48.862; most accessible tissue: Callus, score: 68.272 N N N N
vg0605310329 T -> C LOC_Os06g10320.1 downstream_gene_variant ; 3598.0bp to feature; MODIFIER silent_mutation Average:48.862; most accessible tissue: Callus, score: 68.272 N N N N
vg0605310329 T -> C LOC_Os06g10330.1 downstream_gene_variant ; 2582.0bp to feature; MODIFIER silent_mutation Average:48.862; most accessible tissue: Callus, score: 68.272 N N N N
vg0605310329 T -> C LOC_Os06g10340.1 intron_variant ; MODIFIER silent_mutation Average:48.862; most accessible tissue: Callus, score: 68.272 N N N N