Input data and parameters
Input
| Analysis date: | Tue Oct 31 18:08:09 GMT 2023 | 
| BAM file: | SRX7354403.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): | 53,575,022 / 53,530,134 | 
| Number of aligned pairs (without duplicates): | 53,521,751 | 
| Total number of alignments: | 113,705,171 | 
| Number of secondary alignments: | 6,600,015 | 
| Number of non-unique alignments: | 11,095,750 | 
| Aligned to genes: | 88,668,174 | 
| Ambiguous alignments: | 284,189 | 
| No feature assigned: | 13,266,174 | 
| Missing chromosome in annotation: | 390,884 | 
| Not aligned: | 9,399,940 | 
Reads genomic origin
| Exonic: | 88,668,174 / 86.99% | 
| Intronic: | 8,399,372 / 8.24% | 
| Intergenic: | 4,866,802 / 4.77% | 
| Intronic/intergenic overlapping exon: | 3,678,841 / 3.61% | 
Transcript coverage profile
| 5' bias: | 0.34 | 
| 3' bias: | 0.19 | 
| 5'-3' bias: | 1.96 | 
Junction analysis
| Reads at junctions: | 28,778,570 | 
| ACCT | 5.38% | 
| AGGT | 4.64% | 
| ATCT | 3.75% | 
| TCCT | 3.6% | 
| AGGA | 3.47% | 
| GCCT | 3.25% | 
| AGCT | 2.66% | 
| AGGC | 2.46% | 
| CCCT | 2.41% | 
| AGAT | 2.25% | 
| TTCT | 2.23% | 
 
		
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