Input data and parameters
Report generated by RustQC, a Rust performance-rewrite of Qualimap. Results should be identical to Qualimap v2.3 output.
Input
| Analysis date: | 2026/03/04 18:16:32 |
| BAM file: | /Users/ewels/GitHub/seqera/RustQC/benchmark/input/large/GM12878_REP1.markdup.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | /Users/ewels/GitHub/seqera/RustQC/benchmark/input/large/genes.gtf.gz |
| Number of bases for 5'-3' bias computation: | 100 |
| Number of transcripts for 5'-3' bias computation: | 1,000 |
| Paired-end sequencing: | yes |
| Protocol: | non-strand-specific |
| Sorting performed: | no |
Summary
Reads alignment
| Number of mapped reads (left/right): | 87,559,392 / 87,538,329 |
| Number of aligned pairs (without duplicates): | 174,840,354 |
| Total number of alignments: | 175,097,721 |
| Number of secondary alignments: | 10,620,822 |
| Number of non-unique alignments: | 17,723,193 |
| Aligned to genes: | 9,591,169 |
| Ambiguous alignments: | 332,227 |
| No feature assigned: | 158,071,954 |
| Not aligned: | 0 |
| Strand specificity estimation (fwd/rev): | 33.27% / 66.73% |
Reads genomic origin
| Exonic: | 9,591,169 / 5.72% |
| Intronic: | 105,144,042 / 62.71% |
| Intergenic: | 52,927,912 / 31.57% |
| Intronic/intergenic overlapping exon: | 6,748,550 / 4.03% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.40 |
Junction analysis
| Reads at junctions: | 60,467,173 |
| ACCT | 5.69% |
| AGGT | 5.50% |
| AGGA | 3.56% |
| TCCT | 3.25% |
| ATCT | 3.13% |
| AGGC | 2.93% |
| AGCT | 2.89% |
| GCCT | 2.63% |
| AGGG | 2.35% |
| CCCT | 2.31% |
| AGAT | 2.08% |
Coverage Profile Along Genes (Total)
Coverage Profile Along Genes (Low)
Coverage Profile Along Genes (High)
Coverage Histogram (0-50X)
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