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217   2019-03-17 (日) 10:14:43




@HDThe header line
VN* Format version. Accepted format: /^[0-9]+\.[0-9]+$/.
SO Sorting order of alignments. unknown (default), unsorted, queryname and coordinate
GO Grouping of alignments, indicating that similar alignment records are grouped together ...
@SQReference sequence dictionary.
SN* Reference sequence name.
LN* Reference sequence length
AS Genome assembly identifier
DS Description.
M5 MD5 checksum of the sequence.
SP Species.
UR URI of the sequence.
@RGRead group 詳細は略 
ID* Program record identifier.
PN Program name
CL Command line.
PP Previous @PG-ID. Must match another @PG header’s ID tag.
DS Description.
VN Program version


ColFieldTypeRegexp/RangeBrief description
1QNAMEString[!-?A-~]{1,254}Query template NAME
2FLAGInt[0, 2^16 − 1]bitwise FLAG
3RNAMEStringReference sequence NAME
4POSInt[0, 2^31 − 1]1-based leftmost mapping POSition
5MAPQInt[0, 2^8 − 1]MAPping Quality
6CIGARStringCIGAR string
7RNEXTStringReference name of the mate/next read
8PNEXTInt[0, 2^31 − 1]Position of the mate/next read
9TLENInt[−2^31 + 1, 2^31 − 1]observed Template LENgth
10SEQStringsegment SEQuence
11QUALStringASCII of Phred-scaled base QUALity+33


OpBAMDescription {Consumes queryConsumes reference
M0alignment match (can be a sequence match or mismatch)yesyes
I1insertion to the referenceyesno
D2deletion from the referencenoyes
N3skipped region from the referencenoyes
S4soft clipping (clipped sequences present in SEQ)yesno
H5hard clipping (clipped sequences NOT present in SEQ)nono
P6padding (silent deletion from padded reference)nono
=7sequence matchyesyes
X8sequence mismatchyesyes

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Last-modified: 2019-03-17 (日) 10:14:43 (485d)