Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:51:12 GMT 2023 | 
| BAM file: | SRX7354064.markdup.sorted.bam | 
| Counting algorithm: | uniquely-mapped-reads | 
| GTF file: | gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf | 
| Number of bases for 5'-3' bias computation: | 100 | 
| Number of transcripts for 5'-3' bias computation: | 1,000 | 
| Paired-end sequencing: | yes | 
| Protocol: | strand-specific-reverse | 
| Sorting performed: | yes | 
Summary
Reads alignment
| Number of mapped reads (left/right): | 58,435,666 / 58,324,439 | 
| Number of aligned pairs (without duplicates): | 58,315,493 | 
| Total number of alignments: | 125,651,064 | 
| Number of secondary alignments: | 8,890,959 | 
| Number of non-unique alignments: | 13,939,944 | 
| Aligned to genes: | 90,511,023 | 
| Ambiguous alignments: | 337,133 | 
| No feature assigned: | 19,838,797 | 
| Missing chromosome in annotation: | 1,024,167 | 
| Not aligned: | 16,168,087 | 
Reads genomic origin
| Exonic: | 90,511,023 / 82.02% | 
| Intronic: | 12,266,614 / 11.12% | 
| Intergenic: | 7,572,183 / 6.86% | 
| Intronic/intergenic overlapping exon: | 3,985,199 / 3.61% | 
Transcript coverage profile
| 5' bias: | 0.41 | 
| 3' bias: | 0.32 | 
| 5'-3' bias: | 1.72 | 
Junction analysis
| Reads at junctions: | 35,141,538 | 
| ACCT | 5.07% | 
| AGGT | 4.6% | 
| TCCT | 3.96% | 
| ATCT | 3.74% | 
| GCCT | 3.45% | 
| AGGA | 3.23% | 
| CCCT | 2.77% | 
| AGCT | 2.69% | 
| AGGC | 2.51% | 
| TTCT | 2.21% | 
| AGAT | 1.95% | 
 
		
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