Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:56:25 GMT 2023 | 
| BAM file: | SRX7354127.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): | 76,972,746 / 76,744,382 | 
| Number of aligned pairs (without duplicates): | 76,733,279 | 
| Total number of alignments: | 162,285,685 | 
| Number of secondary alignments: | 8,568,557 | 
| Number of non-unique alignments: | 13,615,947 | 
| Aligned to genes: | 122,737,359 | 
| Ambiguous alignments: | 447,878 | 
| No feature assigned: | 24,530,821 | 
| Missing chromosome in annotation: | 953,680 | 
| Not aligned: | 21,205,742 | 
Reads genomic origin
| Exonic: | 122,737,359 / 83.34% | 
| Intronic: | 17,092,562 / 11.61% | 
| Intergenic: | 7,438,259 / 5.05% | 
| Intronic/intergenic overlapping exon: | 6,544,453 / 4.44% | 
Transcript coverage profile
| 5' bias: | 0.5 | 
| 3' bias: | 0.27 | 
| 5'-3' bias: | 1.66 | 
Junction analysis
| Reads at junctions: | 51,067,445 | 
| ACCT | 5.05% | 
| AGGT | 4.72% | 
| ATCT | 3.66% | 
| TCCT | 3.46% | 
| AGGA | 3.42% | 
| GCCT | 3.38% | 
| AGCT | 2.9% | 
| CCCT | 2.78% | 
| AGGC | 2.5% | 
| AGAT | 2.11% | 
| TTCT | 2.1% | 
 
		
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