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Detailed information for vg1200521899:

Variant ID: vg1200521899 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 521899
Reference Allele: TAlternative Allele: TCTC
Primary Allele: TSecondary Allele: TCTC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGGCCCACTCCGGCTTCGCGACCACCGCCCTGTTTCTGTTGCTGTCACACTGCGCCGTCACCGCGATCGCGTTGGCCTCGTCGACCTGCGATTTCACGT[T/TCTC]
CTCGTCGTCGGTGGACGCCGGGATCAGCACGATCTTCCGGCCGAGCGGGCCGTACACCATGTACAAGGCGGCGACGATGGGGAAGCCGAGGCCGAGCGCC

Reverse complement sequence

GGCGCTCGGCCTCGGCTTCCCCATCGTCGCCGCCTTGTACATGGTGTACGGCCCGCTCGGCCGGAAGATCGTGCTGATCCCGGCGTCCACCGACGACGAG[A/GAGA]
ACGTGAAATCGCAGGTCGACGAGGCCAACGCGATCGCGGTGACGGCGCAGTGTGACAGCAACAGAAACAGGGCGGTGGTCGCGAAGCCGGAGTGGGCCGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of TCTC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.50% 6.40% 0.08% 0.00% NA
All Indica  2759 89.30% 10.60% 0.11% 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 90.60% 9.20% 0.17% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 83.60% 16.30% 0.11% 0.00% NA
Indica Intermediate  786 89.80% 10.10% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg1200521899 T -> TCTC LOC_Os12g01890.1 inframe_insertion ; p.Glu261dup; MODERATE inframe_variant Average:65.914; most accessible tissue: Zhenshan97 flower, score: 84.783 N N N N