The Sequence Alignment/Map Format and SAMtools
Bioinformatics, 2009 · paper · Biomedicine
Describes the Sequence Alignment/Map (SAM) format for storing read alignments from different sequencing platforms, and SAMtools, a companion package of utilities such as indexing, variant calling and alignment viewing. SAM is the format used for 1000 Genomes alignments.
Checked: PDF from europepmc.org, fetched 4 Oct 2026. Page numbers are those of that PDF.
2 findings
Substance Fig. 1c pileup line "ref 14 A 2 .+2AG.+1G" gives depth 2 with two read-base symbols at position 14, but three reads (r001, r002, r003) cover position 14 in Fig. 1a/1b; the depth should be 3 with a third "." for r003.
- p. 2 Fig. 1c, pileup line for position 14
ref 14 A 2 .+2AG.+1G
- p. 2 Fig. 1b, first r003 line
r003 0 ref 9 30 5H6M
- p. 2 Fig. 1c, pileup line for position 13
ref 13 A 3 ...
Judge's note: Checked on a 5x render of Fig. 1 from the PDF. Fig. 1b: r001 POS 7 with 8M2I4M1D3M covers 7-22; r002 POS 9 with 3S6M1P1I4M covers 9-18; r003 POS 9 with 5H6M covers 9-14 (hard clip consumes no reference). Fig. 1a agrees: r003+ AGCTAA sits under ref positions 9-14. The pileup prints depth 3 at positions 9-13 (with r003's mismatch C at position 11) but "ref 14 A 2 .+2AG.+1G", which is r001 and r002 with their insertions only. Every other pileup line checks out (15: 2; 16-18: 3; 19: 2; 20: 2). The caption defines the field as "the number of reads covering the position" and nothing in the paper explains dropping r003 at its last aligned base; "simplified" does not cover it.
Second check: another model agreed
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Substance Fig. 1b prints the SEQ of r001 as "TTAGATAAAGGATACTA", ending in A, while Fig. 1a shows the same read as "TTAGATAAAGGATA*CTG", ending in G (matching reference base G at position 22).
- p. 2 Fig. 1b, first r001 line, SEQ field
TTAGATAAAGGATACTA
- p. 2 Fig. 1a, row r001+
TTAGATAAAGGATA*CTG
Judge's note: Checked on a 5x render of Fig. 1 from the PDF: the last base of the first r001 line in panel (b) is clearly A, and the r001+ row in panel (a) clearly ends CTG. With CIGAR 8M2I4M1D3M at POS 7, the final 3M covers ref 20-22, which the ref row gives as C, T, G. Panel (b) is captioned "The corresponding SAM file", so the two panels should agree. Panel (a) matches the reference and the caption mentions no mismatch for r001, so the A in (b) is the likely error. The pileup in (c) stops at position 20 and cannot settle it independently.
Second check: another model agreed
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3 minor (typos and the like; most checked by the judge only)
Typo Author list prints "1000 Genome Project Data Processing Subgroup" while the abstract ("alignments from the 1000 Genomes Project are released") and the funding statement ("NIH Hapmap/1000 Genomes Project grant") use the plural "Genomes".
- p. 1 Author list
1000 Genome Project Data
- p. 1 Abstract
alignments from the 1000 Genomes Project are released
- p. 2 Funding
Genomes Project grant
- p. 1
1000 Genome Project Data Processing Subgroup
Judge's note: Checked the author-list crop and both full page images. The author line on page 1 reads "1000 Genome Project Data Processing Subgroup"; the abstract on page 1, the funding line on page 2 and the affiliation 7 URL (http://1000genomes.org) all use the plural. The paper is internally inconsistent, so this does not depend on outside knowledge; the singular in the author line is the odd one out.
Second check: another model agreed
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Typo Affiliation 3 prints "Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China"; the institution's name is normally written "Chinese Academy of Sciences".
- p. 1
Chinese Academy of Science, Beijing 100029, China
- p. 1 Affiliation 3
Chinese Academy of Science
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: the official English name of the institution is "Chinese Academy of Sciences" (plural). The page image shows the singular "Chinese Academy of Science" exactly as quoted. Nothing else in the paper names the institution, so the plural form cannot be confirmed from the files.
Second check: another model agreed
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Typo Reference list prints "Langmead,B. et al (2009)" and "Li,H. et al (2008)" without a full stop after "et al", while "Kent,W.J. et al. (2002)" and the in-text citations use "et al.".
- p. 2 References, Langmead entry
Langmead,B. et al (2009)
- p. 2 References, Li entry
Li,H. et al (2008)
- p. 2 References, Kent entry
Kent,W.J. et al. (2002)
- p. 2 References
Langmead,B. et al (2009) Ultrafast
Judge's note: Checked the reference-list crop: the Kent entry has "et al." with a full stop; the Langmead and Li entries have "et al" with none. In-text citations on page 1 ("Langmead et al., 2009; Li et al., 2008", "Kent et al., 2002") all have the full stop. Inconsistent punctuation within one reference list; cosmetic.
Second check: none (judge only)