sam(5)

Okay bestie, let's talk about sam, the manual page you'd find in section 5 under Bioinformatics formats. It's all about the Sequence Alignment/Map file format 🧬✨

🎀 NAME 🎀

sam — Sequence Alignment/Map file format 💖

🌸 DESCRIPTION 🌸

Okay so the Sequence Alignment/Map (SAM) format is TAB-delimited 📋 It's giving very neat rows and columns 💅 Apart from the header lines, which start with the @ symbol, every alignment line has these eleven fixed columns, plus optional extras after them:

• 1 QNAME — Query template/pair NAME 🏷️
• 2 FLAG — bitwise FLAG 🚩
• 3 RNAME — Reference sequence NAME 🧭
• 4 POS — 1-based leftmost POSition/coordinate of clipped sequence 📍
• 5 MAPQ — MAPping Quality (Phred-scaled) 🌟
• 6 CIGAR — extended CIGAR string ✂️
• 7 MRNM — Mate Reference sequence NaMe (= if same as RNAME) 👯
• 8 MPOS — 1-based Mate POSition 📌
• 9 TLEN — inferred Template LENgth (insert size) 📏
• 10 SEQ — query SEQuence on the same strand as the reference 🧬
• 11 QUAL — query QUALity (ASCII-33 gives the Phred base quality) 🫧
• 12+ OPT — variable OPTional fields in the format TAG:VTYPE:VALUE 🧩

🚩 The FLAG field 🚩

Each bit in the FLAG field is its own little vibe ✨ Here's the breakdown, where the second column gives the string representation of the FLAG field:

• 0x0001, p — the read is paired in sequencing 👯‍♀️
• 0x0002, P — the read is mapped in a proper pair 💞
• 0x0004, u — the query sequence itself is unmapped 🙈
• 0x0008, U — the mate is unmapped 💀
• 0x0010, r — strand of the query (1 for reverse) 🔄
• 0x0020, R — strand of the mate 🔁
• 0x0040, 1 — the read is the first read in a pair 🥇
• 0x0080, 2 — the read is the second read in a pair 🥈
• 0x0100, s — the alignment is not primary 🫥
• 0x0200, f — the read fails platform/vendor quality checks ❌
• 0x0400, d — the read is either a PCR or an optical duplicate 👯
• 0x0800, S — the alignment is supplementary 🦋

🔗 SEE ALSO 🔗

• https://github.com/samtools/hts-specs The full SAM/BAM file format specification 📚

htslib, August 2013, sam(5) 🌈 That's the whole tea, bestie, and you're literally ready to read SAM files now 💜🫶