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CompBioBench item

deleterious-mutation-q1

Question

In the paired FASTQs deleterious.mutation.q1.R1.fq.gz and deleterious.mutation.q1.R2.fq.gz (exome 2×150 bp, reads from human chr9 only), there is one gene that harbors a high-confidence homozygous nonsense SNV for a gene that is highly LoF-intolerant. Report the HGNC gene symbol (uppercase) for that gene.

Predicted answer
STXBP1Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Genomics
Question style
Routine Analysis

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 predictionStandard tools only
AnswerSTXBP1
Workflow
Galaxy dataset inspection
Codex GPT-5.5

Replicate 2

Matches predictionUDT-only
AnswerSTXBP1
Workflow
SamtoolsBCFtoolsBedtoolsBWA-MEMMinimap22 more tools
Total tokens
1.0M
Output
14.7K
Codex GPT-5.5

Replicate 3

Matches predictionUDT + standard tools
AnswerSTXBP1
Workflow
Bwa MemSamtools FlagstatSamtools IdxstatsBcftools MpileupBcftools Call8 more tools
Total tokens
4.1M
Output
20.8K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionUDT + standard tools
AnswerSTXBP1
Workflow
Bwa MemSamtools FlagstatFreebayesSnpeff DownloadSnpeff Databases3 more tools
Total tokens
2.7M
Output
9.3K
Codex GPT-5.6 Sol

Replicate 2

Matches predictionStandard tools only
AnswerSTXBP1
Workflow
FastqcBwa MemSamtools FlagstatFreebayesBcftools Filter4 more tools
Total tokens
11.5M
Output
14.9K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionUDT + standard tools
AnswerSTXBP1
Workflow
Bwa MemSamtools StatsGrepFreebayesTp Head Tool5 more tools
Total tokens
6.6M
Output
13.9K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionStandard tools only
AnswerSTXBP1
Workflow
Bwa MemSamtools IdxstatsFreebayesBcftools QueryBcftools Stats3 more tools
Total tokens
4.1M
Output
17.0K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
AnswerSTXBP1
Workflow
Bwa MemSamtools IdxstatsFreebayesPicard AddorreplacereadgroupsSnpeff Databases5 more tools
Total tokens
4.1M
Output
17.5K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionStandard tools only
AnswerSTXBP1
Workflow
Bwa MemSamtools SortFreebayesSnpeff DatabasesSnpeff1 more tools
Total tokens
3.6M
Output
15.6K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionStandard tools only
AnswerSTXBP1
Workflow
FastqcBwa MemFastq Paired End InterlacerSamtools FlagstatSamtools Idxstats
Total tokens
31.5M
Output
65.1K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionStandard tools only
AnswerSTXBP1
Workflow
Bwa Mem2Samtools StatsSamtools FlagstatSamtools IdxstatsBcftools Mpileup6 more tools
Total tokens
8.7M
Output
23.6K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionStandard tools only
AnswerSTXBP1
Workflow
Bwa MemSamtools FlagstatBcftools MpileupBcftools CallSnpeff2 more tools
Total tokens
6.7M
Output
25.3K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMBowtie2SamtoolsBCFtools2 more tools
Codex GPT-5.5

Replicate 2

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMBowtie2Minimap2Samtools4 more tools
Codex GPT-5.5

Replicate 3

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMMinimap2SamtoolsBCFtools2 more tools

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
AnswerSTXBP1
Workflow
Local codeSamtoolsBCFtoolsMinimap2BWA-MEM1 more tools
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMMinimap2SamtoolsBCFtools1 more tools
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMMinimap2SamtoolsBCFtools

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMSamtoolsBCFtoolsMinimap23 more tools
Total tokens
2.7M
Output
21.7K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMSamtoolsBCFtoolsMinimap23 more tools
Total tokens
1.1M
Output
14.1K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMMinimap2SamtoolsBCFtools3 more tools
Total tokens
1.5M
Output
18.7K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMSamtoolsBCFtoolsMinimap22 more tools
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMMinimap2SamtoolsBCFtools3 more tools
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
AnswerSTXBP1
Workflow
Local codeSamtoolsBWA-MEMMinimap2BCFtools3 more tools

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
AnswerSTXBP1
Workflow
Local codeBWA-MEMSamtoolsBCFtoolsMinimap22 more tools
Total tokens
571.1K
Output
4.1K