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CompBioBench item

bam-ops-q1

Question

For the given BAM file mt.sorted.bam, how many reads pass quality threshold of 30 and are properly paired?

Predicted answer
44Most 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
Answer44
Workflow
Samtools View
Total tokens
580.3K
Output
2.4K
Codex GPT-5.5

Replicate 2

Matches predictionStandard tools only
Answer44
Workflow
Samtools View
Total tokens
887.6K
Output
3.7K
Codex GPT-5.5

Replicate 3

Matches predictionStandard tools only
Answer44
Workflow
Samtools View
Total tokens
529.5K
Output
6.0K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionStandard tools only
Answer44
Workflow
Samtools View
Total tokens
473.8K
Output
2.7K
Codex GPT-5.6 Sol

Replicate 2

Matches predictionStandard tools only
Answer44
Workflow
Samtools ViewSamtools Flagstat
Total tokens
500.2K
Output
3.2K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionStandard tools only
Answer44
Workflow
Samtools View
Total tokens
272.5K
Output
2.0K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionStandard tools only
Answer44
Workflow
Samtools View
Total tokens
164.2K
Output
3.0K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
Answer44
Workflow
Samtools ViewSamtools Flagstat
Total tokens
282.1K
Output
4.6K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionStandard tools only
Answer44
Workflow
Samtools ViewSamtools Flagstat
Total tokens
290.9K
Output
5.4K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionStandard tools only
Answer44
Workflow
Samtools View
Total tokens
405.7K
Output
6.7K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionStandard tools only
Answer44
Workflow
Samtools FlagstatSamtools View
Total tokens
633.2K
Output
7.2K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionStandard tools only
Answer44
Workflow
Samtools View
Total tokens
1.2M
Output
14.2K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
Answer44
Workflow
Local codeSamtools
Codex GPT-5.5

Replicate 2

Matches prediction
Answer44
Workflow
Local codeSamtools
Codex GPT-5.5

Replicate 3

Matches prediction
Answer44
Workflow
Local codeSamtools

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
Answer44
Workflow
Local codeSamtools
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
Answer44
Workflow
Local codeSamtools
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
Answer44
Workflow
Local codeSamtools

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
Answer44
Workflow
Local codeSamtools
Total tokens
78.4K
Output
3.1K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
Answer44
Workflow
Local codeSamtoolsPythonpysam
Total tokens
18.1M
Output
70.2K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
Answer44
Workflow
Local codeSamtools
Total tokens
45.4K
Output
1.4K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
Answer44
Workflow
Local codeSamtools
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
Answer44
Workflow
Local codeSamtoolsBedtoolspysam
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
Answer44
Workflow
Local codeSamtools

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
Answer44
Workflow
Local codeSamtools
Total tokens
33.2K
Output
137