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Detailed information for vg0727003953:

Variant ID: vg0727003953 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27003953
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTGCATGGAAATCAAGGAGAACAAATATTTTCCCGGGGAAGAGGTTCAAAAGTTTAAGGTTCAGTCAAATCAGAAGAAGGTTGTTGTTCAATTAACAT[C/T]
GGAGTATACCCGCATCAGTAGGGATCATGCACGCGAGCTCACGAAACGCGCTGAATGTTCCTGCAACAAGTCAAAGCTGCTTCATAAGCCCTGTTCTCAT

Reverse complement sequence

ATGAGAACAGGGCTTATGAAGCAGCTTTGACTTGTTGCAGGAACATTCAGCGCGTTTCGTGAGCTCGCGTGCATGATCCCTACTGATGCGGGTATACTCC[G/A]
ATGTTAATTGAACAACAACCTTCTTCTGATTTGACTGAACCTTAAACTTTTGAACCTCTTCCCCGGGAAAATATTTGTTCTCCTTGATTTCCATGCAGGT

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 98.80% 1.20% 0.00% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 97.40% 2.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 92.30% 7.70% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0727003953 C -> T LOC_Os07g45250.1 missense_variant ; p.Ser630Leu; MODERATE nonsynonymous_codon ; S630L Average:61.592; most accessible tissue: Callus, score: 83.754 unknown unknown TOLERATED 0.12