Input data and parameters
Input
| Analysis date: | Sun Oct 29 13:03:00 GMT 2023 |
| BAM file: | SRX7354193.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): | 48,675,559 / 48,658,801 |
| Number of aligned pairs (without duplicates): | 48,655,482 |
| Total number of alignments: | 103,498,641 |
| Number of secondary alignments: | 6,164,281 |
| Number of non-unique alignments: | 9,590,359 |
| Aligned to genes: | 79,671,351 |
| Ambiguous alignments: | 274,876 |
| No feature assigned: | 13,183,519 |
| Missing chromosome in annotation: | 778,536 |
| Not aligned: | 1,720,638 |
Reads genomic origin
| Exonic: | 79,671,351 / 85.8% |
| Intronic: | 8,715,007 / 9.39% |
| Intergenic: | 4,468,512 / 4.81% |
| Intronic/intergenic overlapping exon: | 3,295,311 / 3.55% |
Transcript coverage profile
| 5' bias: | 0.43 |
| 3' bias: | 0.28 |
| 5'-3' bias: | 1.66 |
Junction analysis
| Reads at junctions: | 29,165,070 |
| ACCT | 4.95% |
| AGGT | 4.58% |
| ATCT | 3.69% |
| TCCT | 3.53% |
| AGGA | 3.37% |
| GCCT | 3.36% |
| AGCT | 2.95% |
| CCCT | 2.66% |
| AGGC | 2.36% |
| TTCT | 2.15% |
| AGAT | 2.04% |

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