Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:30:26 GMT 2023 |
| BAM file: | SRX7354278.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): | 47,216,611 / 47,191,863 |
| Number of aligned pairs (without duplicates): | 47,179,225 |
| Total number of alignments: | 101,573,965 |
| Number of secondary alignments: | 7,165,491 |
| Number of non-unique alignments: | 11,121,565 |
| Aligned to genes: | 80,856,676 |
| Ambiguous alignments: | 344,616 |
| No feature assigned: | 8,435,569 |
| Missing chromosome in annotation: | 815,539 |
| Not aligned: | 3,847,554 |
Reads genomic origin
| Exonic: | 80,856,676 / 90.55% |
| Intronic: | 5,166,134 / 5.79% |
| Intergenic: | 3,269,435 / 3.66% |
| Intronic/intergenic overlapping exon: | 3,864,103 / 4.33% |
Transcript coverage profile
| 5' bias: | 0.1 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 27,218,368 |
| TCCT | 5.73% |
| ACCT | 5.54% |
| ATCT | 4.84% |
| AGGT | 4.02% |
| CCCT | 3.21% |
| AGGA | 2.79% |
| GCCT | 2.44% |
| AGGC | 2.31% |
| TCCC | 2.2% |
| AGCT | 1.97% |
| TTCT | 1.92% |
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