Question
A collaborator sent me variant.status.q1.bam corresponding to a single-end RNA-seq experiment from an individual mapped to hg38. What is the likely variant status at position chrX:154,398,500 (1-based) for this individual? Respond in the format x/y, where x and y are one of A,C,G,T and x<y lexicographically, or x=y if homozygous.
- Inferred answer
C/CUniquely inferred from submitted scores.
- Domain
- Transcriptomics
- 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
IncorrectStandard tools only
AnswerC/T
WorkflowGalaxy dataset inspection
- Total tokens
- 557.3K
- Output
- 5.6K
Codex GPT-5.5
Replicate 2
IncorrectStandard tools only
AnswerC/T
WorkflowSamtools Mpileup→Varscan Mpileup
- Total tokens
- 535.3K
- Output
- 6.4K
Codex GPT-5.5
Replicate 3
IncorrectStandard tools only
AnswerC/T
WorkflowGalaxy dataset inspection
- Total tokens
- 234.9K
- Output
- 3.6K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
IncorrectStandard tools only
AnswerC/T
WorkflowSamtools Mpileup→Bcftools Mpileup→Varscan Mpileup
- Total tokens
- 890.5K
- Output
- 5.0K
Codex GPT-5.6 Sol
Replicate 2
CorrectUDT + standard tools
AnswerC/C
WorkflowSamtools Mpileup→Read-position allele audit chrX 154398500
- Total tokens
- 838.9K
- Output
- 8.2K
Codex GPT-5.6 Sol
Replicate 3
CorrectUDT + standard tools
AnswerC/C
WorkflowSamtools Mpileup→Samtools View→Bcftools Mpileup→Target allele position-aware diagnostic
- Total tokens
- 2.2M
- Output
- 10.2K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
IncorrectStandard tools only
AnswerC/T
WorkflowSamtools Idxstats→Samtools Mpileup
- Total tokens
- 721.7K
- Output
- 10.1K
Codex + DeepSeek-v4-pro-0813
Replicate 2
IncorrectStandard tools only
AnswerC/T
WorkflowSamtools View→Samtools Slice Bam→Extract Genomic Dna 1→Samtools Mpileup→Bcftools Mpileup→1 more tools
- Total tokens
- 5.7M
- Output
- 32.7K
Codex + DeepSeek-v4-pro-0813
Replicate 3
IncorrectStandard tools only
AnswerC/T
WorkflowBcftools Mpileup→Samtools Idxstats→Samtools Mpileup
- Total tokens
- 1.4M
- Output
- 14.3K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
IncorrectStandard tools only
AnswerC/T
WorkflowSamtools Mpileup→Bcftools Mpileup→Samtools Depth
- Total tokens
- 2.4M
- Output
- 14.1K
Codex GPT-5.6 Luna
Replicate 2
IncorrectStandard tools only
AnswerC/T
WorkflowBam To Sam→Samtools Flagstat→Samtools Mpileup→Extract Genomic Dna 1→Fasta2Tab→3 more tools
- Total tokens
- 11.7M
- Output
- 33.5K
Codex GPT-5.6 Luna
Replicate 3
IncorrectStandard tools only
AnswerC/T
- Total tokens
- 1.1M
- Output
- 12.1K