Question
In deleterious.mutation.q2.R1.fq.gz (exome 1×150 bp, reads from human 50Mb chunk of chr9 only), there is one gene that harbors a high-confidence nonsense SNV consistent with somatic mosaicism. The gene is highly LoF-intolerant. Report the HGNC gene symbol (uppercase) for the affected gene, and the approximate alternate allele frequency, rounded to the nearest 10%. Expected output format: POU5F1,10
- Predicted answer
STXBP1,20Most likely answer for this question; not uniquely determined from submitted scores.
- Domain
- Genomics
- Question style
- Synthetic/Augmented Data
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
AnswerSTXBP1,20
WorkflowSamtools→BCFtools→Bedtools→Minimap2→BWA-MEM→1 more tools
- Total tokens
- 517.1K
- Output
- 11.0K
Codex GPT-5.5
Replicate 2
Matches predictionUDT + standard tools
AnswerSTXBP1,20
WorkflowBwa Mem→Samtools Flagstat→Freebayes→Snpeff→Extract stop gained SNVs→2 more tools
- Total tokens
- 2.5M
- Output
- 16.4K
Codex GPT-5.5
Replicate 3
Matches predictionUDT + standard tools
AnswerSTXBP1,20
WorkflowSamtools→BCFtools→Bedtools→BWA-MEM→Minimap2→8 more tools
- Total tokens
- 2.6M
- Output
- 13.1K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
Matches predictionUDT + standard tools
AnswerSTXBP1,20
WorkflowFastqc→Bwa Mem→Samtools Idxstats→Minimap2→BWA-MEM→8 more tools
- Total tokens
- 5.2M
- Output
- 12.5K
Codex GPT-5.6 Sol
Replicate 2
Matches predictionUDT + standard tools
AnswerSTXBP1,20
WorkflowBwa Mem→Samtools Flagstat→Freebayes→Picard Addorreplacereadgroups→Snpeff→7 more tools
- Total tokens
- 24.6M
- Output
- 35.8K
Codex GPT-5.6 Sol
Replicate 3
Matches predictionStandard tools only
AnswerSTXBP1,20
WorkflowBwa Mem→Minimap2→Samtools Flagstat→Samtools Stats→Lofreq Call→3 more tools
- Total tokens
- 13.5M
- Output
- 15.5K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
Matches predictionStandard tools only
AnswerSTXBP1,20
WorkflowBwa Mem→Samtools Flagstat→Samtools Sort→Samtools Stats→Samtools Idxstats→6 more tools
- Total tokens
- 5.0M
- Output
- 24.1K
Codex + DeepSeek-v4-pro-0813
Replicate 2
Matches predictionStandard tools only
AnswerSTXBP1,20
WorkflowBwa Mem→Samtools View→Samtools Idxstats→Bcftools Mpileup→Bcftools Call→5 more tools
- Total tokens
- 9.1M
- Output
- 29.0K
Codex + DeepSeek-v4-pro-0813
Replicate 3
Matches predictionStandard tools only
AnswerSTXBP1,20
WorkflowBwa Mem→Samtools Idxstats→Samtools Flagstat→Freebayes→Picard Addorreplacereadgroups→4 more tools
- Total tokens
- 4.9M
- Output
- 22.5K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
Matches predictionStandard tools only
AnswerSTXBP1,20
WorkflowFastqc→Fastq Info→Bwa→Samtools Flagstat→Samtools Idxstats→9 more tools
- Total tokens
- 20.1M
- Output
- 37.5K
Codex GPT-5.6 Luna
Replicate 2
Matches predictionStandard tools only
AnswerSTXBP1,20
WorkflowFastqc→Bwa Mem→Samtools Flagstat→Samtools Idxstats→Freebayes→6 more tools
- Total tokens
- 9.1M
- Output
- 30.8K
Codex GPT-5.6 Luna
Replicate 3
Matches predictionStandard tools only
AnswerSTXBP1,20
WorkflowBwa Mem→Bowtie2→Samtools Sort→Samtools Flagstat→Samtools Idxstats→5 more tools
- Total tokens
- 4.5M
- Output
- 21.4K