Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:48:56 GMT 2023 |
| BAM file: | SRX7354122.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): | 47,503,427 / 47,469,385 |
| Number of aligned pairs (without duplicates): | 47,457,110 |
| Total number of alignments: | 103,108,919 |
| Number of secondary alignments: | 8,136,107 |
| Number of non-unique alignments: | 12,584,288 |
| Aligned to genes: | 80,039,500 |
| Ambiguous alignments: | 321,738 |
| No feature assigned: | 9,186,051 |
| Missing chromosome in annotation: | 977,342 |
| Not aligned: | 4,500,566 |
Reads genomic origin
| Exonic: | 80,039,500 / 89.7% |
| Intronic: | 5,846,675 / 6.55% |
| Intergenic: | 3,339,376 / 3.74% |
| Intronic/intergenic overlapping exon: | 3,163,504 / 3.55% |
Transcript coverage profile
| 5' bias: | 0.25 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 1.62 |
Junction analysis
| Reads at junctions: | 23,976,346 |
| ACCT | 5.11% |
| AGGT | 4.6% |
| ATCT | 4.17% |
| TCCT | 4.13% |
| AGGA | 3.21% |
| GCCT | 2.95% |
| CCCT | 2.94% |
| AGCT | 2.3% |
| AGGC | 2.21% |
| TTCT | 2.19% |
| AGAA | 1.9% |
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