Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:40:18 GMT 2023 |
| BAM file: | SRX7354086.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): | 34,872,588 / 34,842,289 |
| Number of aligned pairs (without duplicates): | 34,838,712 |
| Total number of alignments: | 74,179,474 |
| Number of secondary alignments: | 4,464,597 |
| Number of non-unique alignments: | 7,493,199 |
| Aligned to genes: | 59,860,018 |
| Ambiguous alignments: | 203,261 |
| No feature assigned: | 6,390,709 |
| Missing chromosome in annotation: | 232,287 |
| Not aligned: | 5,433,491 |
Reads genomic origin
| Exonic: | 59,860,018 / 90.35% |
| Intronic: | 4,484,950 / 6.77% |
| Intergenic: | 1,905,759 / 2.88% |
| Intronic/intergenic overlapping exon: | 2,069,530 / 3.12% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.94 |
Junction analysis
| Reads at junctions: | 22,134,805 |
| ACCT | 5.29% |
| AGGT | 5.03% |
| AGGA | 3.69% |
| TCCT | 3.62% |
| ATCT | 3.61% |
| AGCT | 2.83% |
| AGGC | 2.44% |
| GCCT | 2.4% |
| CCCT | 2.26% |
| AGAT | 2.18% |
| AGGG | 2.08% |
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