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Detailed information for vg0605295245:

Variant ID: vg0605295245 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5295245
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCCACGGGCGCTCCTGCCTCCACGGCTGCTCCGGCGTCCGCGCCGCCGGCGGCCTGGTCCGCATCGTCAGCGGCGCGCGGCACGTCCGCAGCGCGGTGG[G/T]
CCGCTACCTCGCCGCCGCGGACGACGACGAGGAGCACGACGAGCTGTCCGTGGGCGACAAGGTCCTCATCGCCGCCGACGTCGTGGTCGGCCTACGACGT

Reverse complement sequence

ACGTCGTAGGCCGACCACGACGTCGGCGGCGATGAGGACCTTGTCGCCCACGGACAGCTCGTCGTGCTCCTCGTCGTCGTCCGCGGCGGCGAGGTAGCGG[C/A]
CCACCGCGCTGCGGACGTGCCGCGCGCCGCTGACGATGCGGACCAGGCCGCCGGCGGCGCGGACGCCGGAGCAGCCGTGGAGGCAGGAGCGCCCGTGGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.00% 1.70% 0.32% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.20% 4.80% 0.99% 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 99.80% 0.20% 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 88.90% 9.30% 1.83% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0605295245 G -> T LOC_Os06g10300.1 missense_variant ; p.Gly75Val; MODERATE nonsynonymous_codon ; G75V Average:76.871; most accessible tissue: Minghui63 panicle, score: 90.624 unknown unknown DELETERIOUS 0.00