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Detailed information for vg1113568064:

Variant ID: vg1113568064 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 13568064
Reference Allele: GGACATAAlternative Allele: G
Primary Allele: GGACATASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGCTAACTCGTCAGTCTGTTACCCGGCAGAGATAGCGGAGGATGTGCCAGTCAAGATACGGGATTTCTTCATCCCGGTTGACTTTGTGGTGCTGGACAT[GGACATA/G]
GGAAAAGAGACGCCGCTCATCCTGGGTGTCACGCCCTGAAAATCGCCTAAATTAATAATCCATATTTTAAATCATTTTTAGAAATTATTTTAAAAGCCTT

Reverse complement sequence

AAGGCTTTTAAAATAATTTCTAAAAATGATTTAAAATATGGATTATTAATTTAGGCGATTTTCAGGGCGTGACACCCAGGATGAGCGGCGTCTCTTTTCC[TATGTCC/C]
ATGTCCAGCACCACAAAGTCAACCGGGATGAAGAAATCCCGTATCTTGACTGGCACATCCTCCGCTATCTCTGCCGGGTAACAGACTGACGAGTTAGCCA

Allele Frequencies:

Populations Population SizeFrequency of GGACATA(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.20% 2.80% 0.00% 0.00% NA
All Indica  2759 96.20% 3.80% 0.00% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 95.30% 4.70% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 92.70% 7.30% 0.00% 0.00% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1113568064 GGACATA -> G LOC_Os11g23950.1 disruptive_inframe_deletion ; p.Asp57_Ile58del; MODERATE inframe_variant Average:32.036; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N