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Detailed information for vg0500377242:

Variant ID: vg0500377242 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 377242
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCTATCTTGACCAATCTCAGAAATCAGAACCCACCTTGTCCAATCATGTCATGAAACAATCGAATCCCATCACCAGGTTCTCCATACACACAATGGCC[G/A]
ATGATCATTGCGTTCCAGCAAACAACATTCCTAAAGCTCAGCCGATCAAACACCTTCCTCGCAGCATCCGCATTCCGACACTTTCCATACATATCGACCA

Reverse complement sequence

TGGTCGATATGTATGGAAAGTGTCGGAATGCGGATGCTGCGAGGAAGGTGTTTGATCGGCTGAGCTTTAGGAATGTTGTTTGCTGGAACGCAATGATCAT[C/T]
GGCCATTGTGTGTATGGAGAACCTGGTGATGGGATTCGATTGTTTCATGACATGATTGGACAAGGTGGGTTCTGATTTCTGAGATTGGTCAAGATAGCAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.20% 2.80% 0.00% 0.00% NA
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 59.10% 40.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 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
vg0500377242 G -> A LOC_Os05g01635.1 synonymous_variant ; p.Ile335Ile; LOW synonymous_codon Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N