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Detailed information for vg0905621362:

Variant ID: vg0905621362 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5621362
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCTCATCAAAGCGATGACGAAGCTCTCCAATGGCCACCAAAGCTGCCTCCTGACAAGCATGAATATAATCTCTTCCTCCAGCTTCAAACATCATTGAT[G/A]
GAAGGTCTTCACGATCACTAGTCAACGTCATGCGAACACGACTATTCTCCTCATTGGGGTCATGGGGAATTTGGCGATACTCGGGGACAATGTTGTAGCC

Reverse complement sequence

GGCTACAACATTGTCCCCGAGTATCGCCAAATTCCCCATGACCCCAATGAGGAGAATAGTCGTGTTCGCATGACGTTGACTAGTGATCGTGAAGACCTTC[C/T]
ATCAATGATGTTTGAAGCTGGAGGAAGAGATTATATTCATGCTTGTCAGGAGGCAGCTTTGGTGGCCATTGGAGAGCTTCGTCATCGCTTTGATGAGGAG

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 94.30% 5.70% 0.00% 0.00% NA
All Indica  2759 94.60% 5.40% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 56.90% 43.10% 0.00% 0.00% NA
Indica I  595 93.60% 6.40% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 95.00% 5.00% 0.00% 0.00% NA
Indica Intermediate  786 91.90% 8.10% 0.00% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 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
vg0905621362 G -> A LOC_Os09g10310.1 missense_variant ; p.Pro56Leu; MODERATE nonsynonymous_codon ; P56L Average:44.224; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 benign 0.617 DELETERIOUS 0.04