Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:26:58 GMT 2023 |
| BAM file: | SRX7354305.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): | 48,357,489 / 48,321,369 |
| Number of aligned pairs (without duplicates): | 48,307,671 |
| Total number of alignments: | 105,170,663 |
| Number of secondary alignments: | 8,491,805 |
| Number of non-unique alignments: | 12,842,435 |
| Aligned to genes: | 82,044,639 |
| Ambiguous alignments: | 342,911 |
| No feature assigned: | 8,856,386 |
| Missing chromosome in annotation: | 1,084,292 |
| Not aligned: | 3,282,692 |
Reads genomic origin
| Exonic: | 82,044,639 / 90.26% |
| Intronic: | 5,437,612 / 5.98% |
| Intergenic: | 3,418,774 / 3.76% |
| Intronic/intergenic overlapping exon: | 4,056,545 / 4.46% |
Transcript coverage profile
| 5' bias: | 0.11 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 1.84 |
Junction analysis
| Reads at junctions: | 30,145,166 |
| ACCT | 5.34% |
| TCCT | 5.06% |
| AGGT | 4.47% |
| ATCT | 4.08% |
| AGGA | 3.02% |
| CCCT | 2.91% |
| GCCT | 2.35% |
| AGGC | 2.22% |
| AGCT | 2.03% |
| TTCT | 1.9% |
| TCCC | 1.89% |
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