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Detailed information for vg0521979033:

Variant ID: vg0521979033 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 21979033
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 368. )

Flanking Sequence (100 bp) in Reference Genome:


ATGAAAAATCAGTTATCTTTGGATGATGGTGACAATAGTAGAGAAGCTCCGAAGCGAGCAGCTAGGCATAAATCAAGGTCTACTGTATTGACTGAAGATG[G/C]
AAACGAAGATGTTGGTGGAGGTGATGAGGACAGTGAGTATGACGTGCCAAGTGAGGACGAGGGTGGAAATTTGACTGCTGATATACTTCCACCGTTGAAA

Reverse complement sequence

TTTCAACGGTGGAAGTATATCAGCAGTCAAATTTCCACCCTCGTCCTCACTTGGCACGTCATACTCACTGTCCTCATCACCTCCACCAACATCTTCGTTT[C/G]
CATCTTCAGTCAATACAGTAGACCTTGATTTATGCCTAGCTGCTCGCTTCGGAGCTTCTCTACTATTGTCACCATCATCCAAAGATAACTGATTTTTCAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 0.30% 2.20% 0.00% NA
All Indica  2759 96.00% 0.50% 3.48% 0.00% NA
All Japonica  1512 99.70% 0.10% 0.20% 0.00% NA
Aus  269 98.90% 0.00% 1.12% 0.00% NA
Indica I  595 91.90% 1.00% 7.06% 0.00% NA
Indica II  465 96.60% 0.00% 3.44% 0.00% NA
Indica III  913 98.40% 0.50% 1.10% 0.00% NA
Indica Intermediate  786 96.10% 0.40% 3.56% 0.00% NA
Temperate Japonica  767 99.50% 0.10% 0.39% 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 96.70% 1.10% 2.22% 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
vg0521979033 G -> C LOC_Os05g37540.1 missense_variant ; p.Gly705Ala; MODERATE nonsynonymous_codon ; G705A Average:7.775; most accessible tissue: Zhenshan97 flower, score: 12.818 unknown unknown TOLERATED 0.13