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Detailed information for vg0135986031:

Variant ID: vg0135986031 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35986031
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAAAATTCTAACAATGTCACTTGTCATAAAGGATAGGTAGGCATTCAAAACCAATGTTTTCCAGTGTTTCAGATCATTTCAGCAATCAGGGAAGCTCA[G/C]
AATAAATATCACTAACGACTTCAAGAATTCAAAAATATATTGTCTATGTTTTTGTAAGAACATGTATGATCAAAATAAGAATACAGCAGCCAGACAAATA

Reverse complement sequence

TATTTGTCTGGCTGCTGTATTCTTATTTTGATCATACATGTTCTTACAAAAACATAGACAATATATTTTTGAATTCTTGAAGTCGTTAGTGATATTTATT[C/G]
TGAGCTTCCCTGATTGCTGAAATGATCTGAAACACTGGAAAACATTGGTTTTGAATGCCTACCTATCCTTTATGACAAGTGACATTGTTAGAATTTTCAA

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 98.20% 1.80% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 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 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 26.00% 74.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0135986031 G -> C LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:35.036; most accessible tissue: Callus, score: 69.06 N N N N