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Detailed information for vg1113568107:

Variant ID: vg1113568107 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 13568107
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGCCAGTCAAGATACGGGATTTCTTCATCCCGGTTGACTTTGTGGTGCTGGACATGGACATAGGAAAAGAGACGCCGCTCATCCTGGGTGTCACGCCC[T/C]
GAAAATCGCCTAAATTAATAATCCATATTTTAAATCATTTTTAGAAATTATTTTAAAAGCCTTCAAGTTAAACTCTAATAATCTAGGAAAAATTTCAGCA

Reverse complement sequence

TGCTGAAATTTTTCCTAGATTATTAGAGTTTAACTTGAAGGCTTTTAAAATAATTTCTAAAAATGATTTAAAATATGGATTATTAATTTAGGCGATTTTC[A/G]
GGGCGTGACACCCAGGATGAGCGGCGTCTCTTTTCCTATGTCCATGTCCAGCACCACAAAGTCAACCGGGATGAAGAAATCCCGTATCTTGACTGGCACA

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 99.50% 0.50% 0.00% 0.00% NA
All Indica  2759 99.40% 0.60% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 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
vg1113568107 T -> C LOC_Os11g23950.1 stop_lost&splice_region_variant ; p.Ter71Argext*?; HIGH stop_lost Average:28.107; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 N N N N