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Detailed information for vg0202540584:

Variant ID: vg0202540584 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2540584
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTCTAGAAAGTATTTTTCAGGAACAATTGAGCACTTGAGTAGGATGTGGTCGAGTACACTGCATTATCAAGAACGTTCTTGACAAATGCAGAGTCGTC[G/A]
CGCCCAACCAACCAACGAAGACCGACGACCTATCTCATACACCGGCCATGGCTGGACTACTCGAGAAAAGGTTGTTAACGGATAATTGCTCACGAACAAT

Reverse complement sequence

ATTGTTCGTGAGCAATTATCCGTTAACAACCTTTTCTCGAGTAGTCCAGCCATGGCCGGTGTATGAGATAGGTCGTCGGTCTTCGTTGGTTGGTTGGGCG[C/T]
GACGACTCTGCATTTGTCAAGAACGTTCTTGATAATGCAGTGTACTCGACCACATCCTACTCAAGTGCTCAATTGTTCCTGAAAAATACTTTCTAGAAGG

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 95.80% 4.10% 0.02% 0.00% NA
All Indica  2759 96.90% 3.10% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 95.80% 4.20% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.20% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0202540584 G -> A LOC_Os02g05290.1 missense_variant ; p.Ala67Thr; MODERATE nonsynonymous_codon ; A67T Average:56.313; most accessible tissue: Minghui63 panicle, score: 73.225 unknown unknown TOLERATED 0.10