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Detailed information for vg0905620973:

Variant ID: vg0905620973 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5620973
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGGAATAGCTGGCAACGATCTAACGAGGCACTAATCCCGCCTTGCGTCGAAGCGAAGAGATGGATCTTCTTCCTCTGGAATAGCTGGCTCTCTTTCTT[C/T]
TGGATCTTCCTCCTCTGGGGTAGCTGACGGCGGTGCTTCTCCCTTGAGCTCGGCCAGTTCCTTCTGCAGGCGATACACCTTGCTTTCTAGCTTGCAAATC

Reverse complement sequence

GATTTGCAAGCTAGAAAGCAAGGTGTATCGCCTGCAGAAGGAACTGGCCGAGCTCAAGGGAGAAGCACCGCCGTCAGCTACCCCAGAGGAGGAAGATCCA[G/A]
AAGAAAGAGAGCCAGCTATTCCAGAGGAAGAAGATCCATCTCTTCGCTTCGACGCAAGGCGGGATTAGTGCCTCGTTAGATCGTTGCCAGCTATTCCAGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.80% 2.20% 0.00% 0.00% NA
All Indica  2759 97.40% 2.60% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 87.40% 12.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 93.80% 6.20% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 95.40% 4.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0905620973 C -> T LOC_Os09g10310.1 missense_variant ; p.Glu186Lys; MODERATE nonsynonymous_codon ; E186K Average:52.628; most accessible tissue: Zhenshan97 flag leaf, score: 67.31 unknown unknown TOLERATED 0.14