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Detailed information for vg1124757052:

Variant ID: vg1124757052 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24757052
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGGCGGCGATGGCGCAGCACCTGCTGGTGGCGGCGGACAGGTACGACATGGAGAGGCTGAAGAAGGTGTGCGAGGACAGGATGGTCAGGCACCTCGACG[T/C]
CGGCACGGCGGCGACGTCGCTGGCGTTGGCCGAGCAGCACGATTGCCCTGAGCTCAAGAAGGCCATCCTGAGGTTCATGGCGTCGCCGGCGAGGTTGAAG

Reverse complement sequence

CTTCAACCTCGCCGGCGACGCCATGAACCTCAGGATGGCCTTCTTGAGCTCAGGGCAATCGTGCTGCTCGGCCAACGCCAGCGACGTCGCCGCCGTGCCG[A/G]
CGTCGAGGTGCCTGACCATCCTGTCCTCGCACACCTTCTTCAGCCTCTCCATGTCGTACCTGTCCGCCGCCACCAGCAGGTGCTGCGCCATCGCCGCCGC

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 95.60% 4.40% 0.00% 0.00% NA
All Indica  2759 97.80% 2.20% 0.00% 0.00% NA
All Japonica  1512 98.50% 1.50% 0.00% 0.00% NA
Aus  269 55.80% 44.20% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 97.70% 2.30% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1124757052 T -> C LOC_Os11g41300.1 missense_variant ; p.Val296Ala; MODERATE nonsynonymous_codon ; V296A Average:74.037; most accessible tissue: Zhenshan97 young leaf, score: 83.199 benign 0.248 TOLERATED 0.85