Input data and parameters
Input
| Analysis date: | Tue Oct 31 12:08:44 GMT 2023 |
| BAM file: | SRX7354363.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): | 34,741,126 / 34,709,660 |
| Number of aligned pairs (without duplicates): | 34,704,178 |
| Total number of alignments: | 74,030,807 |
| Number of secondary alignments: | 4,580,021 |
| Number of non-unique alignments: | 7,514,933 |
| Aligned to genes: | 57,238,542 |
| Ambiguous alignments: | 191,903 |
| No feature assigned: | 8,707,180 |
| Missing chromosome in annotation: | 378,249 |
| Not aligned: | 4,389,570 |
Reads genomic origin
| Exonic: | 57,238,542 / 86.8% |
| Intronic: | 5,554,891 / 8.42% |
| Intergenic: | 3,152,289 / 4.78% |
| Intronic/intergenic overlapping exon: | 2,179,623 / 3.31% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.93 |
Junction analysis
| Reads at junctions: | 16,977,865 |
| ACCT | 5.57% |
| AGGT | 4.66% |
| ATCT | 3.56% |
| AGGA | 3.53% |
| TCCT | 3.42% |
| GCCT | 3.34% |
| AGCT | 2.67% |
| CCCT | 2.48% |
| AGGC | 2.34% |
| AGAT | 2.23% |
| TTCT | 2.14% |

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