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Detailed information for vg0141375811:

Variant ID: vg0141375811 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41375811
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCTGTCCGCGGCCGGCTTCGGCAAGATCAAGGTGTCCACGGCCGTCAAGATGGACGTGCTCGGCACCTCGTCGCCGCCCTCCGGCGGCGAGTTCAGCGA[C/T]
GCCGCCGTCATGGCCCCCATCGCGAAGTTCTTGGCGAGCAACGGCTCGCCGCTGCTGGCCAACGTCTACCCCTACTTCGCCTACAAGGGCGGCGACGTCG

Reverse complement sequence

CGACGTCGCCGCCCTTGTAGGCGAAGTAGGGGTAGACGTTGGCCAGCAGCGGCGAGCCGTTGCTCGCCAAGAACTTCGCGATGGGGGCCATGACGGCGGC[G/A]
TCGCTGAACTCGCCGCCGGAGGGCGGCGACGAGGTGCCGAGCACGTCCATCTTGACGGCCGTGGACACCTTGATCTTGCCGAAGCCGGCCGCGGACAGCG

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 94.40% 5.60% 0.02% 0.00% NA
All Indica  2759 90.40% 9.50% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 79.70% 20.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 87.80% 12.20% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 3.90% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 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
vg0141375811 C -> T LOC_Os01g71410.1 synonymous_variant ; p.Asp202Asp; LOW synonymous_codon Average:71.566; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N