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Detailed information for vg0702285881:

Variant ID: vg0702285881 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 2285881
Reference Allele: TAlternative Allele: TTCC
Primary Allele: TSecondary Allele: TTCC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTTTTTTGGGTTGTGACATATATATATATATATATGTATATATATATATATAATTTTCTAATAATCTACTCGAACGCCCATGTGTTCTCCTTGCGGAT[T/TTCC]
TCCTCCTCCTCCGGCGTGAAGTCGTTCTTGATCCCAAACTCCTTCCTGATCTGCTCCGGCGACTTGCCTTTGATCAGGTTCGCCGTGTGCTGGCAGCACA

Reverse complement sequence

TGTGCTGCCAGCACACGGCGAACCTGATCAAAGGCAAGTCGCCGGAGCAGATCAGGAAGGAGTTTGGGATCAAGAACGACTTCACGCCGGAGGAGGAGGA[A/GGAA]
ATCCGCAAGGAGAACACATGGGCGTTCGAGTAGATTATTAGAAAATTATATATATATATATACATATATATATATATATATGTCACAACCCAAAAAAGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of TTCC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.00% 1.70% 0.32% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 94.20% 4.90% 0.86% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 97.90% 0.80% 1.30% 0.00% NA
Tropical Japonica  504 86.70% 12.90% 0.40% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0702285881 T -> TTCC LOC_Os07g05150.1 disruptive_inframe_insertion ; p.Glu147dup; MODERATE inframe_variant Average:49.588; most accessible tissue: Zhenshan97 panicle, score: 86.058 N N N N