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Detailed information for vg0209797014:

Variant ID: vg0209797014 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 9797014
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:


GAACGTGGAGAGGGATGCGGAGGGGAACCAGCAGGGGCACGTGGAAAGGGATGTGGAGGGGAACCAGGAGGAGGAGGCTAGTGGTAGTCAACCCTCCGTT[G/T]
GACAGAAGAGGGCACGCGGGCAACGAGGTGCAGCGAAGAAGCTTGAGGGTCGGCACATCATAACGGAAGTGGAAGAAGATGGACGTCCTAGTGCCCCGGC

Reverse complement sequence

GCCGGGGCACTAGGACGTCCATCTTCTTCCACTTCCGTTATGATGTGCCGACCCTCAAGCTTCTTCGCTGCACCTCGTTGCCCGCGTGCCCTCTTCTGTC[C/A]
AACGGAGGGTTGACTACCACTAGCCTCCTCCTCCTGGTTCCCCTCCACATCCCTTTCCACGTGCCCCTGCTGGTTCCCCTCCGCATCCCTCTCCACGTTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 0.80% 0.10% 28.42% 70.63% NA
All Indica  2759 0.80% 0.00% 15.48% 83.69% NA
All Japonica  1512 0.80% 0.30% 51.26% 47.62% NA
Aus  269 0.00% 0.00% 16.36% 83.64% NA
Indica I  595 0.70% 0.00% 9.92% 89.41% NA
Indica II  465 1.10% 0.00% 14.62% 84.30% NA
Indica III  913 0.70% 0.00% 17.52% 81.82% NA
Indica Intermediate  786 1.00% 0.00% 17.81% 81.17% NA
Temperate Japonica  767 0.80% 0.40% 43.68% 55.15% NA
Tropical Japonica  504 0.80% 0.20% 60.71% 38.29% NA
Japonica Intermediate  241 0.80% 0.40% 55.60% 43.15% NA
VI/Aromatic  96 2.10% 1.00% 67.71% 29.17% NA
Intermediate  90 2.20% 0.00% 35.56% 62.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0209797014 G -> T LOC_Os02g17110.1 stop_gained ; p.Gly73*; HIGH stop_gained Average:5.689; most accessible tissue: Zhenshan97 flower, score: 12.818 N N N N
vg0209797014 G -> DEL LOC_Os02g17110.1 N frameshift_variant Average:5.689; most accessible tissue: Zhenshan97 flower, score: 12.818 N N N N