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Detailed information for vg0234310447:

Variant ID: vg0234310447 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 34310447
Reference Allele: ACTCAlternative Allele: A
Primary Allele: ACTCSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTGGACATTGGAGATTGTGTGAAGCTCTCGTAATCAAAGTTCACGAAGTCCTCTTTGGTGAAAACAGGATTTTCTCCACAGACCTTGCAAGTTGGTGA[ACTC/A]
CTACTGATCTTGACCTGCAGGAGTTTGTGTAACCGTTTATGGCCTTTCAGGGAGATTGAAACAGAGGATTCTGATGGTTGCTGTTTAGGAAATTGAGTCG

Reverse complement sequence

CGACTCAATTTCCTAAACAGCAACCATCAGAATCCTCTGTTTCAATCTCCCTGAAAGGCCATAAACGGTTACACAAACTCCTGCAGGTCAAGATCAGTAG[GAGT/T]
TCACCAACTTGCAAGGTCTGTGGAGAAAATCCTGTTTTCACCAAAGAGGACTTCGTGAACTTTGATTACGAGAGCTTCACACAATCTCCAATGTCCAAAA

Allele Frequencies:

Populations Population SizeFrequency of ACTC(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.10% 1.50% 0.36% 0.00% NA
All Indica  2759 96.80% 2.60% 0.62% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 1.00% 0.84% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 93.60% 5.00% 1.40% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0234310447 ACTC -> A LOC_Os02g56050.1 disruptive_inframe_deletion ; p.Arg11del; MODERATE inframe_variant Average:55.08; most accessible tissue: Callus, score: 80.669 N N N N