Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:42:07 GMT 2023 | 
| BAM file: | SRX7354260.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): | 51,903,999 / 51,867,385 | 
| Number of aligned pairs (without duplicates): | 51,855,078 | 
| Total number of alignments: | 109,821,579 | 
| Number of secondary alignments: | 6,050,195 | 
| Number of non-unique alignments: | 10,073,428 | 
| Aligned to genes: | 85,488,259 | 
| Ambiguous alignments: | 262,474 | 
| No feature assigned: | 13,528,892 | 
| Missing chromosome in annotation: | 468,526 | 
| Not aligned: | 5,658,446 | 
Reads genomic origin
| Exonic: | 85,488,259 / 86.34% | 
| Intronic: | 9,367,011 / 9.46% | 
| Intergenic: | 4,161,881 / 4.2% | 
| Intronic/intergenic overlapping exon: | 4,194,168 / 4.24% | 
Transcript coverage profile
| 5' bias: | 0.3 | 
| 3' bias: | 0.16 | 
| 5'-3' bias: | 1.87 | 
Junction analysis
| Reads at junctions: | 27,726,423 | 
| ACCT | 5.55% | 
| AGGT | 4.67% | 
| ATCT | 3.55% | 
| AGGA | 3.53% | 
| GCCT | 3.25% | 
| TCCT | 3.21% | 
| AGCT | 2.78% | 
| AGAT | 2.39% | 
| AGGC | 2.39% | 
| CCCT | 2.29% | 
| TTCT | 2.18% | 
 
		
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