SAM-format

The two records in the SAM-format represent two reads that are part of a pair from the sequencing data. Below is the analysis of these two records:

Record 1 VH00358:89:AAFC5MTM5:1:1101:62048:1038_:N:0:TTTCTCTA+CTCGACG 83 NZ_AKKR01000009 78640 60 110M20S = 78640-110 ATCATAACCGTCGGCTGAATAAGCAAGATTATAAAACCCTCACTCTGGCGGCTTTAGGCGGAGCGCTTGAGTTTTATGACTTCATTATTTTCGTTTTCTTTGCTGCGGTTGATGAGAGCGGGGGTGTAGG * NM:i:0 MD:Z:110 MC:Z:110M20S AS:i:110 XS:i:0

Record 2 VH00358:89:AAFC5MTM5:1:1101:62048:1038_:N:0:TTTCTCTA+CTCGACG 163 NZ_AKKR01000009 78640 60 110M20S = 78640110 ATCATAACCGTCGGCTGAATAAGCAAGATTATAAAACCCTCACTCTGGCGGCTTTAGGCGGAGCGCTTGAGTTTTATGACTTCATTATTTTCGTTTTCTTTGCTGCGGTTGATGAGAGCTTTGTTGTAGG * NM:i:0 MD:Z:110 MC:Z:110M20S AS:i:110 XS:i:0

Analysis

• Read Names: Both reads have the same name: VH00358:89:AAFC5MTM5:1:1101:62048:1038_:N:0:TTTCTCTA+CTCGACG. This indicates they are part of the same pair.

• Flags: First Record (83): 83 indicates the read is the second read in the pair (0x40 is not set), and it is mapped in reverse complement (0x10 is set). It also indicates that the read is part of a properly paired alignment (0x2 is set). Second Record (163): 163 indicates the read is the first read in the pair (0x40 is set), and it is mapped in reverse complement (0x10 is set). It also indicates that the read is part of a properly paired alignment (0x2 is set).

• Reference Name: Both reads are mapped to the same reference sequence: NZ_AKKR01000009.

• Position: Both reads are mapped to the same position: 78640.

• Mapping Quality: Both reads have a mapping quality score of 60, which indicates high confidence in the mapping.

• CIGAR String: Both reads have the same CIGAR string: 110M20S. This means the first 110 bases are matched/mismatched (alignment) and the last 20 bases are soft-clipped (not aligned to the reference).

• Mate Information: The = symbol indicates that the mate is mapped to the same reference. The 78640-110 and 78640110 values indicate the positions of the mates.

• Sequence: The sequences are nearly identical for the aligned parts: Record 1: ATCATAACCGTCGGCTGAATAAGCAAGATTATAAAACCCTCACTCTGGCGGCTTTAGGCGGAGCGCTTGAGTTTTATGACTTCATTATTTTCGTTTTCTTTGCTGCGGTTGATGAGAGCGGGGGTGTAGG Record 2: ATCATAACCGTCGGCTGAATAAGCAAGATTATAAAACCCTCACTCTGGCGGCTTTAGGCGGAGCGCTTGAGTTTTATGACTTCATTATTTTCGTTTTCTTTGCTGCGGTTGATGAGAGCTTTGTTGTAGG

• Optional Fields: NM:i:0: Number of mismatches is 0. MD:Z:110: Mismatch string indicating no mismatches in the 110 aligned bases. MC:Z:110M20S: CIGAR string for the mate. AS:i:110: Alignment score for the read. XS:i:0: Suboptimal alignment score.

Conclusion

These two SAM records represent a pair of reads mapped to the same position on the reference sequence NZ_AKKR01000009. Both reads are aligned with high confidence (mapping quality 60), and they have no mismatches in the aligned portion of their sequences. The 110M20S CIGAR string indicates that the first 110 bases are aligned, and the last 20 bases are soft-clipped. Both reads are reverse complemented.

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