Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:31:28 GMT 2023 |
| BAM file: | SRX7354315.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): | 50,541,327 / 50,501,007 |
| Number of aligned pairs (without duplicates): | 50,496,485 |
| Total number of alignments: | 107,373,695 |
| Number of secondary alignments: | 6,331,361 |
| Number of non-unique alignments: | 10,718,986 |
| Aligned to genes: | 87,240,060 |
| Ambiguous alignments: | 258,539 |
| No feature assigned: | 8,719,573 |
| Missing chromosome in annotation: | 436,537 |
| Not aligned: | 4,942,102 |
Reads genomic origin
| Exonic: | 87,240,060 / 90.91% |
| Intronic: | 4,484,289 / 4.67% |
| Intergenic: | 4,235,284 / 4.41% |
| Intronic/intergenic overlapping exon: | 3,319,745 / 3.46% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.9 |
Junction analysis
| Reads at junctions: | 26,824,098 |
| ACCT | 5.27% |
| AGGT | 4.64% |
| ATCT | 3.55% |
| AGGA | 3.55% |
| TCCT | 3.35% |
| GCCT | 3.14% |
| AGCT | 2.79% |
| AGGC | 2.38% |
| TTCT | 2.28% |
| AGAT | 2.26% |
| CCCT | 2.24% |

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