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Detailed information for vg1124757078:

Variant ID: vg1124757078 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24757078
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTGGCGGCGGACAGGTACGACATGGAGAGGCTGAAGAAGGTGTGCGAGGACAGGATGGTCAGGCACCTCGACGTCGGCACGGCGGCGACGTCGCTGGCG[T/C]
TGGCCGAGCAGCACGATTGCCCTGAGCTCAAGAAGGCCATCCTGAGGTTCATGGCGTCGCCGGCGAGGTTGAAGGCGGTCATGGCGAGCGATGGGTATGA

Reverse complement sequence

TCATACCCATCGCTCGCCATGACCGCCTTCAACCTCGCCGGCGACGCCATGAACCTCAGGATGGCCTTCTTGAGCTCAGGGCAATCGTGCTGCTCGGCCA[A/G]
CGCCAGCGACGTCGCCGCCGTGCCGACGTCGAGGTGCCTGACCATCCTGTCCTCGCACACCTTCTTCAGCCTCTCCATGTCGTACCTGTCCGCCGCCACC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 2.50% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 65.40% 34.60% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 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 87.50% 12.50% 0.00% 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
vg1124757078 T -> C LOC_Os11g41300.1 synonymous_variant ; p.Leu305Leu; LOW synonymous_codon Average:72.07; most accessible tissue: Zhenshan97 young leaf, score: 82.077 N N N N