|
gptkbp:instanceOf
|
file format
|
|
gptkbp:alignmentSectionBeginsWith
|
no special character
|
|
gptkbp:alignmentSectionContains
|
one line per alignment
|
|
gptkbp:alignmentSectionField1
|
QNAME (query template name)
|
|
gptkbp:alignmentSectionField10
|
SEQ (segment sequence)
|
|
gptkbp:alignmentSectionField11
|
QUAL (ASCII of Phred-scaled base quality plus 33)
|
|
gptkbp:alignmentSectionField2
|
FLAG (bitwise flag)
|
|
gptkbp:alignmentSectionField3
|
RNAME (reference sequence name)
|
|
gptkbp:alignmentSectionField4
|
POS (1-based leftmost mapping position)
|
|
gptkbp:alignmentSectionField5
|
MAPQ (mapping quality)
|
|
gptkbp:alignmentSectionField6
|
CIGAR (CIGAR string)
|
|
gptkbp:alignmentSectionField7
|
RNEXT (reference name of the mate/next read)
|
|
gptkbp:alignmentSectionField8
|
PNEXT (position of the mate/next read)
|
|
gptkbp:alignmentSectionField9
|
TLEN (observed template length)
|
|
gptkbp:canBeCompressedAs
|
gptkb:BAM_file_format
|
|
gptkbp:canBeIndexedAs
|
gptkb:BAM_file_format
|
|
gptkbp:canStore
|
paired-end reads
single-end reads
chimeric alignments
secondary alignments
supplementary alignments
|
|
gptkbp:CIGARStringDescribes
|
alignment operations
|
|
gptkbp:commonIn
|
gptkb:SAMtools
|
|
gptkbp:contains
|
header section
alignment section
|
|
gptkbp:convertedTo
|
gptkb:BAM_file_format
gptkb:CRAM_file_format
|
|
gptkbp:developedBy
|
gptkb:The_SAM/BAM_Format_Specification_Working_Group
|
|
gptkbp:fieldsSeparatedBy
|
tab
|
|
gptkbp:fileExtension
|
.sam
|
|
gptkbp:firstReleased
|
2009
|
|
gptkbp:fullName
|
Sequence Alignment/Map format
|
|
gptkbp:hasBinaryVersion
|
gptkb:BAM_file_format
|
|
gptkbp:headerSectionBeginsWith
|
@
|
|
https://www.w3.org/2000/01/rdf-schema#label
|
SAM file format
|
|
gptkbp:numberOfMandatoryFields
|
11
|
|
gptkbp:optionalFieldsFormat
|
TAG:TYPE:VALUE
|
|
gptkbp:qualityScoresFormat
|
Phred quality
|
|
gptkbp:referenceGenomeIndicatedBy
|
header section
|
|
gptkbp:relatedTo
|
gptkb:BAM_file_format
gptkb:CRAM_file_format
gptkb:VCF_file_format
|
|
gptkbp:specifies
|
https://samtools.github.io/hts-specs/SAMv1.pdf
|
|
gptkbp:standardizedBy
|
true
|
|
gptkbp:supportsCIGARString
|
true
|
|
gptkbp:supportsOptionalFields
|
true
|
|
gptkbp:supportsPairedEndReads
|
true
|
|
gptkbp:supportsQualityScores
|
true
|
|
gptkbp:supportsUnmappedReads
|
true
|
|
gptkbp:text
|
true
|
|
gptkbp:usedBy
|
Illumina sequencing data
Oxford Nanopore sequencing data
PacBio sequencing data
next-generation sequencing data analysis tools
|
|
gptkbp:usedFor
|
representing aligned nucleotide sequences
storing biological sequence alignment data
|
|
gptkbp:usedIn
|
genomics
bioinformatics
|
|
gptkbp:bfsParent
|
gptkb:BAM_file_format
gptkb:CRAM_file_format
|
|
gptkbp:bfsLayer
|
8
|