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Detailed information for vg0118270638:

Variant ID: vg0118270638 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18270638
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.20, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


TGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTG[G/A]
TTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGTGGTGTAGGAGATTGCTACGT

Reverse complement sequence

ACGTAGCAATCTCCTACACCACAACCTCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAA[C/T]
CAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCA

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 77.30% 22.20% 0.53% 0.00% NA
All Indica  2759 61.80% 37.40% 0.83% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.90% 0.70% 0.37% 0.00% NA
Indica I  595 90.60% 9.20% 0.17% 0.00% NA
Indica II  465 51.80% 48.00% 0.22% 0.00% NA
Indica III  913 48.40% 50.10% 1.53% 0.00% NA
Indica Intermediate  786 61.30% 37.80% 0.89% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 1.11% 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
vg0118270638 G -> A LOC_Os01g33180.1 stop_gained ; p.Trp64*; HIGH stop_gained Average:52.524; most accessible tissue: Minghui63 young leaf, score: 70.038 N N N N