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Detailed information for vg0503843879:

Variant ID: vg0503843879 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 3843879
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAAATAGGGGACATTCTCGTTGGTGATGGAGCTATAGTCCGTGGAGCTCGACGCGGCGGCGTACACCGCCGTCGTCGACGACGACGACGCCGATGCCGG[C/T]
AGCGTCGCCGTCGTCACTACCCCCATGGTGCCAGCAACGGGCAGCTGGCGTGCGGCGGCGGCGGCGGCGAGGAGGTGCGAGGCGTGGGAGGAAGGGAGCA

Reverse complement sequence

TGCTCCCTTCCTCCCACGCCTCGCACCTCCTCGCCGCCGCCGCCGCCGCACGCCAGCTGCCCGTTGCTGGCACCATGGGGGTAGTGACGACGGCGACGCT[G/A]
CCGGCATCGGCGTCGTCGTCGTCGACGACGGCGGTGTACGCCGCCGCGTCGAGCTCCACGGACTATAGCTCCATCACCAACGAGAATGTCCCCTATTTTA

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 99.00% 1.00% 0.00% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 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 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 96.60% 3.40% 0.00% 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
vg0503843879 C -> T LOC_Os05g07270.1 synonymous_variant ; p.Leu173Leu; LOW synonymous_codon Average:79.272; most accessible tissue: Zhenshan97 root, score: 86.579 N N N N