Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:30:27 GMT 2023 |
| BAM file: | SRX7354054.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): | 27,832,575 / 27,813,922 |
| Number of aligned pairs (without duplicates): | 27,810,680 |
| Total number of alignments: | 58,945,548 |
| Number of secondary alignments: | 3,299,051 |
| Number of non-unique alignments: | 5,345,654 |
| Aligned to genes: | 47,396,075 |
| Ambiguous alignments: | 166,979 |
| No feature assigned: | 5,729,011 |
| Missing chromosome in annotation: | 307,829 |
| Not aligned: | 1,993,029 |
Reads genomic origin
| Exonic: | 47,396,075 / 89.22% |
| Intronic: | 3,666,499 / 6.9% |
| Intergenic: | 2,062,512 / 3.88% |
| Intronic/intergenic overlapping exon: | 1,909,329 / 3.59% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.2 |
Junction analysis
| Reads at junctions: | 14,714,661 |
| ACCT | 5.54% |
| AGGT | 4.61% |
| ATCT | 3.81% |
| TCCT | 3.55% |
| GCCT | 3.51% |
| AGGA | 3.34% |
| CCCT | 2.5% |
| AGCT | 2.49% |
| TTCT | 2.36% |
| AGGC | 2.34% |
| AGAT | 2.01% |

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