Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:58:55 GMT 2023 |
| BAM file: | SRX7354373.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): | 44,530,709 / 44,460,156 |
| Number of aligned pairs (without duplicates): | 44,455,117 |
| Total number of alignments: | 95,735,349 |
| Number of secondary alignments: | 6,744,484 |
| Number of non-unique alignments: | 10,579,769 |
| Aligned to genes: | 71,136,528 |
| Ambiguous alignments: | 262,281 |
| No feature assigned: | 12,978,644 |
| Missing chromosome in annotation: | 778,127 |
| Not aligned: | 7,438,063 |
Reads genomic origin
| Exonic: | 71,136,528 / 84.57% |
| Intronic: | 7,488,293 / 8.9% |
| Intergenic: | 5,490,351 / 6.53% |
| Intronic/intergenic overlapping exon: | 2,904,588 / 3.45% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.37 |
| 5'-3' bias: | 1.67 |
Junction analysis
| Reads at junctions: | 26,188,065 |
| ACCT | 5.31% |
| AGGT | 4.5% |
| TCCT | 3.96% |
| ATCT | 3.64% |
| GCCT | 3.35% |
| AGGA | 3.28% |
| CCCT | 2.79% |
| AGCT | 2.68% |
| AGGC | 2.38% |
| TTCT | 2.15% |
| AGAT | 1.99% |
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