Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:19:54 GMT 2023 |
| BAM file: | SRX7354061.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): | 44,847,581 / 44,822,597 |
| Number of aligned pairs (without duplicates): | 44,813,520 |
| Total number of alignments: | 96,368,813 |
| Number of secondary alignments: | 6,698,635 |
| Number of non-unique alignments: | 10,701,358 |
| Aligned to genes: | 76,980,781 |
| Ambiguous alignments: | 307,655 |
| No feature assigned: | 7,756,371 |
| Missing chromosome in annotation: | 622,648 |
| Not aligned: | 3,137,260 |
Reads genomic origin
| Exonic: | 76,980,781 / 90.85% |
| Intronic: | 4,954,938 / 5.85% |
| Intergenic: | 2,801,433 / 3.31% |
| Intronic/intergenic overlapping exon: | 3,403,529 / 4.02% |
Transcript coverage profile
| 5' bias: | 0.15 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.76 |
Junction analysis
| Reads at junctions: | 23,887,359 |
| ACCT | 5.23% |
| TCCT | 4.86% |
| AGGT | 4.53% |
| ATCT | 4.31% |
| AGGA | 3.23% |
| CCCT | 2.96% |
| GCCT | 2.64% |
| AGGC | 2.2% |
| TTCT | 2.19% |
| AGCT | 2.13% |
| AGAA | 1.89% |

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