Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:14:11 GMT 2023 |
| BAM file: | SRX7354168.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): | 39,647,906 / 39,626,495 |
| Number of aligned pairs (without duplicates): | 39,623,385 |
| Total number of alignments: | 84,451,008 |
| Number of secondary alignments: | 5,176,607 |
| Number of non-unique alignments: | 8,437,724 |
| Aligned to genes: | 67,877,665 |
| Ambiguous alignments: | 231,390 |
| No feature assigned: | 7,478,344 |
| Missing chromosome in annotation: | 425,885 |
| Not aligned: | 2,399,353 |
Reads genomic origin
| Exonic: | 67,877,665 / 90.08% |
| Intronic: | 4,885,422 / 6.48% |
| Intergenic: | 2,592,922 / 3.44% |
| Intronic/intergenic overlapping exon: | 2,346,326 / 3.11% |
Transcript coverage profile
| 5' bias: | 0.29 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.77 |
Junction analysis
| Reads at junctions: | 22,286,107 |
| ACCT | 5.35% |
| AGGT | 4.49% |
| ATCT | 3.66% |
| GCCT | 3.46% |
| TCCT | 3.42% |
| AGGA | 3.37% |
| AGCT | 2.72% |
| AGGC | 2.34% |
| CCCT | 2.33% |
| TTCT | 2.15% |
| AGAT | 2.07% |
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