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Detailed information for vg0825998516:

Variant ID: vg0825998516 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25998516
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTGCACAGAGTGAAGATGGTTTACCATCTTTGTTCATCAAGAAGACCTCAAAGATAACATTGATCTTGGGGTCGATCTCAGTAAGCAGCAGGAAGACAG[C/A]
GATGTACTCACCATTACGGCCCTCACATCCACGCGGGAATAACAAAATCGTCGCATTGTGCTCCCCGGCCGAGATTCTTATTCCGGGCAAGCACTCGCCG

Reverse complement sequence

CGGCGAGTGCTTGCCCGGAATAAGAATCTCGGCCGGGGAGCACAATGCGACGATTTTGTTATTCCCGCGTGGATGTGAGGGCCGTAATGGTGAGTACATC[G/T]
CTGTCTTCCTGCTGCTTACTGAGATCGACCCCAAGATCAATGTTATCTTTGAGGTCTTCTTGATGAACAAAGATGGTAAACCATCTTCACTCTGTGCAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.60% 0.10% 0.28% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 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% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 89.60% 0.00% 10.42% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0825998516 C -> A LOC_Os08g41150.1 missense_variant ; p.Ala62Ser; MODERATE nonsynonymous_codon ; A62S Average:57.249; most accessible tissue: Zhenshan97 young leaf, score: 66.32 unknown unknown TOLERATED 1.00