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CompBioBench item

variant-coordinate-lookup-q1

Question

Retrieve the single base genomic position for the following variant identifiers: rs200533370, rs241311, NM_006492.3:c.595-2A>T, CA548798891, VCV000587372.6, OMIM 616787.0001 on the GRCh38 reference assembly. Report in semi-colon separated chr#:position format (1-based, inclusive), no spaces (e.g. chr1:2;chr2:34).

Predicted answer
chrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Genomics
Question style
Retrieval

An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.

Galaxy

12/12 terminal item results

UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches predictionUDT-only
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Variant position lookupVariant position lookup diagnosticsVariant position source diagnosticsVariant position lookup final
Total tokens
1.8M
Output
18.5K
Galaxy historyAgent trace
Codex GPT-5.5

Replicate 2

Matches predictionUDT-only
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Resolve variant positions GRCh38Resolve variant positions GRCh38 v2Resolve variant positions GRCh38 v3Resolve variant positions GRCh38 v4Resolve variant positions GRCh38 v52 more tools
Total tokens
2.4M
Output
24.9K
Galaxy historyAgent trace
Codex GPT-5.5

Replicate 3

Matches predictionUDT-only
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Variant Coordinate LookupVariant Coordinate Lookup v2UDT Mechanical ProbeUDT Doc ProbeData Fetch
Total tokens
3.0M
Output
19.1K
Galaxy historyAgent trace

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionUDT-only
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Galaxy UDTvariant_lookupVariant lookupPublic variant reference lookupdbSNP public reference lookup1 more tools
Total tokens
2.5M
Output
11.7K
Galaxy historyAgent trace
Codex GPT-5.6 Sol

Replicate 2

Matches predictionUDT-only
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Authoritative variant source auditAuthoritative variant source follow-upExtract and cross-check variant coordinate candidatesFinal GRCh38 variant positions
Total tokens
1.2M
Output
11.0K
Galaxy historyAgent trace
Codex GPT-5.6 Sol

Replicate 3

Matches predictionUDT-only
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Probe authoritative variant sourcesRetrieve authoritative variant recordsExtract decisive variant record fieldsProbe intronic HGVS sourcesFinalize GRCh38 variant coordinates
Total tokens
2.7M
Output
13.8K
Galaxy historyAgent trace

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionUDT + standard tools
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Gprofiler SnpenseVariant Position Resolver
Total tokens
3.7M
Output
22.4K
Galaxy historyAgent trace
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionUDT-only
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Variant ID GRCh38 Resolver
Total tokens
5.9M
Output
30.0K
Galaxy historyAgent trace
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionUDT + standard tools
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Gprofiler SnpenseVariant Lookup RawCat UDT ProbeUpload1Regex11 more tools
Total tokens
14.2M
Output
43.3K
Galaxy historyAgent trace

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionUDT + standard tools
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Variant coordinate diagnosticVariant coordinate diagnostic v2Variant UDT runtime probeRegex1Tp Grep Tool
Total tokens
10.4M
Output
34.7K
Galaxy historyAgent trace
Codex GPT-5.6 Luna

Replicate 2

Matches predictionNo analysis tools recorded
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Upload1
Total tokens
18.7M
Output
36.2K
Galaxy historyAgent trace
Codex GPT-5.6 Luna

Replicate 3

Matches predictionUDT-only
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Fetch authoritative variant recordsFetch authoritative variant records v2Inspect variant record placementsDiagnose ClinVar XML placementsFetch authoritative variant records v312 more tools
Galaxy historyAgent trace

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local code
Agent trace
Codex GPT-5.5

Replicate 2

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local code
Agent trace
Codex GPT-5.5

Replicate 3

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local code
Agent trace

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local code
Agent trace
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local codePython
Agent trace
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local code
Agent trace

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local codePython
Total tokens
527.4K
Output
7.0K
Agent trace
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local codePython
Total tokens
4.0M
Output
25.9K
Agent trace
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local codePython
Total tokens
439.2K
Output
5.5K
Agent trace

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local code
Agent trace
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local code
Agent trace
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local code
Agent trace

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
AnswerchrX:47574285;chr1:228858538;chr1:110061565;chr3:181712343;chr10:102685872;chr16:3523261
Workflow
Local codePython
Total tokens
100.5K
Output
1.3K
Agent trace