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Detailed information for vg0727002986:

Variant ID: vg0727002986 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27002986
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGATCGTATATTTTGGTCACCTGCACCGTGCGTACTGGCCTTTACATACTGTCGTCCTGTGCTTTGCATCAAGGGCACTTCACTATGTGGGAAATACCAA[C/T]
CACTTCTGTTAACTGCTCTAGCATTAGATGCTAATGATAACTTGATTCCAGTAGCATTTGCCATCATTGAAGGTGAGAGCAAGGAGAGCTGGCTGTGGTT

Reverse complement sequence

AACCACAGCCAGCTCTCCTTGCTCTCACCTTCAATGATGGCAAATGCTACTGGAATCAAGTTATCATTAGCATCTAATGCTAGAGCAGTTAACAGAAGTG[G/A]
TTGGTATTTCCCACATAGTGAAGTGCCCTTGATGCAAAGCACAGGACGACAGTATGTAAAGGCCAGTACGCACGGTGCAGGTGACCAAAATATACGATCG

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 99.30% 0.60% 0.06% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 97.90% 1.90% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.30% 0.26% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 10.00% 0.41% 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
vg0727002986 C -> T LOC_Os07g45250.1 missense_variant ; p.Pro308Ser; MODERATE nonsynonymous_codon ; P308S Average:61.906; most accessible tissue: Callus, score: 85.205 benign -1.472 TOLERATED 0.15