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Called By
Filter
SNP   INDEL CNV
[Step1] General option
Known snp Effect

[Step2] Quality option
  QUAL     Allele count in genotypes  

QUAL >

AC >

[Step3] Sample option
Sample

A01  A05  A12  A14  A16  A23  A27  A28  A44  A45  A46  A48  
N26093  N26100  N26104  N26113  N27007  N27010  N29016  N29079  N29082  N308  N303  

[Step4] Output option
Separate By

Definition followed GATK homepage
REF/ALT: The reference base and alternative base that vary in the samples, or in the population in general. Note that REF and ALT are always given on the forward strand. For indels the REF and ALT bases always include at least one base each (the base before the event).
QUAL: The Phred scaled probability of Probability that REF/ALT polymorphism exists at this site given sequencing data. Because the Phred scale is -10 * log(1-p), a value of 10 indicates a 1 in 10 chance of error, while a 100 indicates a 1 in 10^10 chance. These values can grow very large when a large amount of NGS data is used for variant calling.
Phred quality scores are logarithmically linked to error probailities.
Phred Quality Score Probability of incorrect base call Base call accuracy
101 in 1090%
201 in 10099%
301 in 100099.9%
401 in 1000099.99%
501 in 10000099.999%
AC: Allele count in genotypes, for each ALT allele, in the same order as listed.(Max value is 46.because we have 23 individual.)
EFF: Effects are predicted by snpEff
Impact: Effects are categorized by 'impact': {High, Moderate, Low, Modifier}. The categories are as follows:
ImpactEffects
HighSPLICE SITE ACCEPTOR
SPLICE SITE DONOR
START LOST
EXON DELETED
FRAME SHIFT
STOP GAINED
STOP LOST
RARE AMINO ACID
ModerateNON SYNONYMOUS CODING
CODON CHANGE
CODON INSERTION
CODON CHANGE PLUS CODON INSERTION
CODON DELETION
CODON CHANGE PLUS CODON DELETION
UTR 5 DELETED
UTR 3 DELETED
LowSYNONYMOUS START
NON SYNONYMOUS START
START GAINED
SYNONYMOUS CODING
SYNONYMOUS STOP
ModifierUTR 5 PRIME
UTR 3 PRIME
REGULATION
UPSTREAM
DOWNSTREAM
GENE
TRANSCRIPT
EXON
INTRON CONSERVED
INTRON
INTRAGENIC
INTERGENIC
INTERGENIC CONSERVED
NONE
CHROMOSOME
CUSTOM
CDS
* at CNV information
Position: Start coordinate of this variant
REF: Reference base at Position
END: End coordinate of this variant
SVLEN: DIfference in length between REF and ALT alleles
SVTYPE: Type of structural variant