Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:18:19 GMT 2023 |
| BAM file: | SRX7354076.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): | 47,851,335 / 47,822,950 |
| Number of aligned pairs (without duplicates): | 47,812,514 |
| Total number of alignments: | 105,792,541 |
| Number of secondary alignments: | 10,118,256 |
| Number of non-unique alignments: | 14,817,796 |
| Aligned to genes: | 80,687,414 |
| Ambiguous alignments: | 397,717 |
| No feature assigned: | 8,225,760 |
| Missing chromosome in annotation: | 1,663,854 |
| Not aligned: | 3,201,471 |
Reads genomic origin
| Exonic: | 80,687,414 / 90.75% |
| Intronic: | 4,879,503 / 5.49% |
| Intergenic: | 3,346,257 / 3.76% |
| Intronic/intergenic overlapping exon: | 3,827,583 / 4.3% |
Transcript coverage profile
| 5' bias: | 0.06 |
| 3' bias: | 0.08 |
| 5'-3' bias: | 2.29 |
Junction analysis
| Reads at junctions: | 24,925,098 |
| TCCT | 6.55% |
| ACCT | 5.56% |
| CCCT | 5.33% |
| ATCT | 4.79% |
| AGGT | 3.7% |
| AGGA | 2.72% |
| GTCT | 2.41% |
| AGAC | 2.24% |
| AGGC | 2.17% |
| TCCG | 2.11% |
| GCCT | 1.89% |
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