Result

3.30E‐3 proportion

Evidence concern: excluded from comparisons

Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing'

song2025-zymo-kraken-native-db-galaxy proportion (relative abundance of Pseudomonas aeruginosa)

Tested configuration: Kraken (Song et al. 2025)
Protocol: Relative abundance of each species in ZymoBIOMICS Standard II against its theoretical distribution (Song et al. 2025 Table 1)
Dataset: ZymoBIOMICS Microbial Community Standard II positive control (Song et al. 2025)
Procedure: dna-pathogen-20261009-protocol-song2025-zymo-abundance
Evaluation: Kraken on ZymoBIOMICS Standard II (Song et al. 2025)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedDiagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, row 'Pseudomonas aeruginosa', column 'Kraken'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Single positive control
Adaptation: Native database per pipeline
Scoring implementation: Relative abundance as output by each pipeline

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-8cc1db47c7f9
Property and statement	Original source and location	Review and provenance
Reported result 3.30E‐3 Individual claims	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ Table 1, row 'Pseudomonas aeruginosa', column 'Kraken' Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Extracted by deterministic parse of the pinned Europe PMC full-text XML (extract/extract_pathogen.py), with every row and column label asserted. printed_value is the table cell text exactly as in the XML. Pending independent review. Independent review 2026-10-09: value and identity match the source. Kraken column of Table 1 is under an evidence concern on the source. Field: `attributes.printed_value` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Extraction artifact

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Sources and history

Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

1 source records and release history

Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Original source · MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML

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Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261009-result-song2025-zymo-kraken-native-db-galaxy-pseudomonas-aeruginosa

metric: proportion
metric direction: unknown
unit: fraction
printed value: 3.30E‐3
numeric value: 0.00330
source locator: Table 1, row 'Pseudomonas aeruginosa', column 'Kraken'
metric qualifier: relative abundance of Pseudomonas aeruginosa
unit detail: relative abundance printed in E notation (theoretical value in column 'Theoretical')
missing metadata: uncertainty: reason: unreported
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: 7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12705909/fullTextXML; method note: Re-downloaded the article XML and matched its SHA-256. Read Song Table 1 with a separate parser written for this review (row and column spans expanded; the extractor's script was not run). Checked printed and numeric value, locator, metric, qualifier, unit and direction from the headers, and the evaluation's configuration, protocol and dataset.; note: Extracted by deterministic parse of the pinned Europe PMC full-text XML (extract/extract_pathogen.py), with every row and column label asserted. printed_value is the table cell text exactly as in the XML. Pending independent review. Independent review 2026-10-09: value and identity match the source. Kraken column of Table 1 is under an evidence concern on the source.

Related records

evaluation: Kraken on ZymoBIOMICS Standard II (Song et al. 2025)

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