Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:26:21 GMT 2023 |
| BAM file: | SRX7354243.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): | 48,630,098 / 48,581,987 |
| Number of aligned pairs (without duplicates): | 48,570,598 |
| Total number of alignments: | 103,895,805 |
| Number of secondary alignments: | 6,683,720 |
| Number of non-unique alignments: | 10,743,495 |
| Aligned to genes: | 83,213,850 |
| Ambiguous alignments: | 331,531 |
| No feature assigned: | 9,000,876 |
| Missing chromosome in annotation: | 606,053 |
| Not aligned: | 11,984,909 |
Reads genomic origin
| Exonic: | 83,213,850 / 90.24% |
| Intronic: | 5,023,006 / 5.45% |
| Intergenic: | 3,977,870 / 4.31% |
| Intronic/intergenic overlapping exon: | 3,500,552 / 3.8% |
Transcript coverage profile
| 5' bias: | 0.15 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.01 |
Junction analysis
| Reads at junctions: | 29,500,473 |
| ACCT | 5.08% |
| TCCT | 4.83% |
| AGGT | 4.55% |
| ATCT | 4.45% |
| CCCT | 3.33% |
| AGGA | 3.24% |
| GCCT | 2.47% |
| TTCT | 2.25% |
| AGGC | 2.16% |
| AGCT | 2.15% |
| AGAA | 1.97% |

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