1. SAM file

SAM file is a format to save alignment information of short reads mapped against reference sequences.

##---------------View SAM file
$ cat P3-VERO-P3-1-vero_L4.sam | head -n 10
# or
$ samtools view -h P3-VERO-P3-1-vero_L4.sam | head -n 10

A SAM file usually starts with a header section and is followed by alignment information as tab-separated lines for each read.

* Header section

Each header line begins with the character @ followed by one of the two-letter header record type codes defined in this section.

@SQ    SN:NC_045512.2    LN:29903
@PG    ID:bwa    PN:bwa    VN:0.7.17-r1188    CL:bwa mem -t 4 -M /public/home/ykk/SARS_CoV_2/mapping/ref/Wuhan-Hu-1.fasta /public/home/ykk/SARS_CoV_2/clean_datP3-1-vero_L4_1.fq.gz /public/home/ykk/SARS_CoV_2/clean_data/P3-VERO-P3-1-vero_L4_2.fq.gz

* Tab-delimited read alignment information lines

Each alignment line typically represents the linear alignment of a segment. Each line consists of 11 or more TAB-separated fields.

A00821:275:HWMMWDSXX:4:1101:1298:1016    83    NC_045512.2    4209    60    150M    =    4179    -180    AAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTAGGGTTTAAATGGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTATTATCTCTAATGAGAAGC    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF    NM:i:0    MD:Z:150    MC:Z:150M    AS:i:150
……
A00821:275:HWMMWDSXX:4:1101:23484:2519    77    *    0    0    *    *    0    0    ACGGATTGTACGCAAGTACAGTGGTAGGGGAGCGTTCCAAGGGTGATGATAAGGACTGGTGGAGCGCTTGGAAGTGATTATGCCGGCATGAGTAACGTTTGGAAGTGAGAATCTTCCATGCCGTTTGACCAAGGTTTCCT    FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFFF:FFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF    AS:i:0    XS:i:0

The first eleven fields are always present and in the order shown below; if the information represented by any of these fields is unavailable, that field’s value will be a placeholder, either ‘0’ or ‘*’ as determined by the field’s type.

* The Meaning of Each Column

1. QNAME: Read Name
2. FLAG: Combination of bitwise FLAGs. Each bit is explained in the following table:
   
3. RNAME: Reference sequence NAME of the alignment.
4. POS: 1-based leftmost mapping position of the first CIGAR operation that “consumes” a reference base (see table below). The fifirst base in a reference sequence has coordinate 1. POS is set as 0 for an unmapped read without coordination.
5. MAPQ: Mapping quality.
6. CIGAR: The CIGAR operations are given in the following table (set ‘*’ if unavailable):
   
7. RNEXT: Reference sequence name of the primary alignment of the NEXT read in the template. This field is set as ‘*’ when the information is unavailable, and set as ‘=’ if RNEXT is identical to RNAME.
8. PNEXT: 1-based Position of the primary alignment of the NEXT read in the template. Set as 0 when the information is unavailable.
9. TLEN: The length of the template.
10. SEQ: Read Sequence
11. QUAL: Read Quality

    2. BAM file

    A BAM file (*.bam) is the compressed binary version of a SAM file.

    View BAM file

    BAM files can only be viewed by samtools view command.

$ samtools view -h P3-VERO-P3-1-vero_L4_sort.bam | head -n 10

@HD    VN:1.6    SO:coordinate
@SQ    SN:NC_045512.2    LN:29903
@PG    ID:bwa    PN:bwa    VN:0.7.17-r1188    CL:bwa mem -t 4 -M /public/home/ykk/SARS_CoV_2/mapping/ref/Wuhan-Hu-1.fasta /public/home/ykk/SARS_CoV_2/clean_data/P3-VERO-P3-1-vero_L4_1.fq.gz /public/home/ykk/SARS_CoV_2/clean_data/P3-VERO-P3-1-vero_L4_2.fq.gz
@PG    ID:samtools    PN:samtools    PP:bwa    VN:1.11    CL:samtools view -b -F 12 /public/home/ykk/SARS_CoV_2/mapping/P3-VERO-P3-1-vero_L4.sam
@PG    ID:samtools.1    PN:samtools    PP:samtools    VN:1.11    CL:samtools sort -@ 4 -l 9 -o /public/home/ykk/SARS_CoV_2/sortedbam/P3-VERO-P3-1-vero_L4_sort.bam /public/home/ykk/SARS_CoV_2/bam/P3-VERO-P3-1-vero_L4.bam
@PG    ID:samtools.2    PN:samtools    PP:samtools.1    VN:1.12    CL:samtools view -h P3-VERO-P3-1-vero_L4_sort.bam
A00821:275:HWMMWDSXX:4:1116:11957:9580    163    NC_045512.2    1    60    92M    =    1    92    ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGC    ,FFFF:F:FFFF:FFF:FFFFFF:FFFFFFFFFFFFFFFF:FFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F   NM:i:0    MD:Z:92    MC:Z:92M    AS:i:92    XS:i:0

3. More information:

• http://samtools.github.io/hts-specs/SAMv1.pdf
• https://blog.csdn.net/zhu_si_tao/article/details/53436351
• https://blog.csdn.net/genome_denovo/article/details/78712972?utm_medium=distribute.pc_relevant.none-task-blog-2~default~BlogCommendFromBaidu~default-4.control&dist_request_id=&depth_1-utm_source=distribute.pc_relevant.none-task-blog-2~default~BlogCommendFromBaidu~default-4.control