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Detailed information for vg1124756905:

Variant ID: vg1124756905 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24756905
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGCCGGTGTTCAGGGCGGAGCTCCTCGGCCCCATGAGGGAGCACGCCGCGACGACCATCCGCGTCGACGACATGGACGCCTCCGTGTTCGCCGCTCTGC[T/C]
GCGCTTCGTCTACACCGACGAGCTGCCGGAGCTGGACGGCGGCAGCGCGGCGGCGATGGCGCAGCACCTGCTGGTGGCGGCGGACAGGTACGACATGGAG

Reverse complement sequence

CTCCATGTCGTACCTGTCCGCCGCCACCAGCAGGTGCTGCGCCATCGCCGCCGCGCTGCCGCCGTCCAGCTCCGGCAGCTCGTCGGTGTAGACGAAGCGC[A/G]
GCAGAGCGGCGAACACGGAGGCGTCCATGTCGTCGACGCGGATGGTCGTCGCGGCGTGCTCCCTCATGGGGCCGAGGAGCTCCGCCCTGAACACCGGCGA

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 97.40% 2.50% 0.08% 0.00% NA
All Indica  2759 99.20% 0.80% 0.04% 0.00% NA
All Japonica  1512 93.70% 6.10% 0.20% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 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 97.50% 2.40% 0.13% 0.00% NA
Temperate Japonica  767 94.50% 5.20% 0.26% 0.00% NA
Tropical Japonica  504 96.40% 3.60% 0.00% 0.00% NA
Japonica Intermediate  241 85.50% 14.10% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1124756905 T -> C LOC_Os11g41300.1 missense_variant ; p.Leu247Pro; MODERATE nonsynonymous_codon ; L247P Average:73.673; most accessible tissue: Minghui63 flag leaf, score: 84.028 probably damaging 2.468 DELETERIOUS 0.00