Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:15:53 GMT 2023 |
| BAM file: | SRX7354256.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): | 37,203,698 / 37,186,377 |
| Number of aligned pairs (without duplicates): | 37,183,663 |
| Total number of alignments: | 79,228,672 |
| Number of secondary alignments: | 4,838,597 |
| Number of non-unique alignments: | 8,154,609 |
| Aligned to genes: | 62,331,193 |
| Ambiguous alignments: | 207,418 |
| No feature assigned: | 8,243,786 |
| Missing chromosome in annotation: | 291,666 |
| Not aligned: | 2,044,763 |
Reads genomic origin
| Exonic: | 62,331,193 / 88.32% |
| Intronic: | 5,469,862 / 7.75% |
| Intergenic: | 2,773,924 / 3.93% |
| Intronic/intergenic overlapping exon: | 2,457,941 / 3.48% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 19,930,593 |
| ACCT | 5.28% |
| AGGT | 4.82% |
| AGGA | 3.65% |
| ATCT | 3.46% |
| TCCT | 3.4% |
| GCCT | 2.98% |
| AGCT | 2.76% |
| AGGC | 2.48% |
| CCCT | 2.47% |
| AGAT | 2.32% |
| TTCT | 2.09% |
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