Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:42:56 GMT 2023 | 
| BAM file: | SRX7354250.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): | 40,119,530 / 40,095,269 | 
| Number of aligned pairs (without duplicates): | 40,091,153 | 
| Total number of alignments: | 85,136,767 | 
| Number of secondary alignments: | 4,921,968 | 
| Number of non-unique alignments: | 7,899,604 | 
| Aligned to genes: | 66,538,643 | 
| Ambiguous alignments: | 272,396 | 
| No feature assigned: | 9,935,478 | 
| Missing chromosome in annotation: | 490,646 | 
| Not aligned: | 3,188,711 | 
Reads genomic origin
| Exonic: | 66,538,643 / 87.01% | 
| Intronic: | 5,955,768 / 7.79% | 
| Intergenic: | 3,979,710 / 5.2% | 
| Intronic/intergenic overlapping exon: | 3,002,008 / 3.93% | 
Transcript coverage profile
| 5' bias: | 0.38 | 
| 3' bias: | 0.31 | 
| 5'-3' bias: | 1.61 | 
Junction analysis
| Reads at junctions: | 24,181,798 | 
| ACCT | 5.12% | 
| AGGT | 4.71% | 
| ATCT | 3.62% | 
| TCCT | 3.6% | 
| GCCT | 3.43% | 
| AGGA | 3.26% | 
| CCCT | 2.68% | 
| AGCT | 2.65% | 
| AGGC | 2.48% | 
| TTCT | 2.41% | 
| AGAT | 1.92% | 
 
		
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