Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:36:33 GMT 2023 | 
| BAM file: | SRX7354344.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): | 38,731,464 / 38,697,306 | 
| Number of aligned pairs (without duplicates): | 38,693,744 | 
| Total number of alignments: | 82,525,911 | 
| Number of secondary alignments: | 5,097,141 | 
| Number of non-unique alignments: | 8,680,446 | 
| Aligned to genes: | 65,071,975 | 
| Ambiguous alignments: | 240,079 | 
| No feature assigned: | 8,244,553 | 
| Missing chromosome in annotation: | 288,858 | 
| Not aligned: | 3,129,702 | 
Reads genomic origin
| Exonic: | 65,071,975 / 88.75% | 
| Intronic: | 5,229,003 / 7.13% | 
| Intergenic: | 3,015,550 / 4.11% | 
| Intronic/intergenic overlapping exon: | 2,409,472 / 3.29% | 
Transcript coverage profile
| 5' bias: | 0.31 | 
| 3' bias: | 0.2 | 
| 5'-3' bias: | 1.85 | 
Junction analysis
| Reads at junctions: | 19,444,197 | 
| ACCT | 5.34% | 
| AGGT | 4.6% | 
| ATCT | 3.68% | 
| TCCT | 3.67% | 
| AGGA | 3.46% | 
| GCCT | 3.34% | 
| AGCT | 2.64% | 
| CCCT | 2.61% | 
| AGGC | 2.44% | 
| AGAT | 2.23% | 
| TTCT | 2.16% | 
		
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