Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:31:41 GMT 2023 |
| BAM file: | SRX7354229.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): | 44,844,239 / 44,797,146 |
| Number of aligned pairs (without duplicates): | 44,769,178 |
| Total number of alignments: | 96,009,021 |
| Number of secondary alignments: | 6,367,636 |
| Number of non-unique alignments: | 9,800,127 |
| Aligned to genes: | 73,782,606 |
| Ambiguous alignments: | 305,705 |
| No feature assigned: | 11,336,793 |
| Missing chromosome in annotation: | 783,790 |
| Not aligned: | 1,449,497 |
Reads genomic origin
| Exonic: | 73,782,606 / 86.68% |
| Intronic: | 8,322,545 / 9.78% |
| Intergenic: | 3,014,248 / 3.54% |
| Intronic/intergenic overlapping exon: | 3,847,373 / 4.52% |
Transcript coverage profile
| 5' bias: | 0.47 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 28,163,303 |
| ACCT | 5.04% |
| AGGT | 4.7% |
| ATCT | 3.65% |
| TCCT | 3.6% |
| AGGA | 3.43% |
| GCCT | 3.02% |
| AGCT | 2.77% |
| CCCT | 2.66% |
| AGGC | 2.39% |
| AGAT | 2.06% |
| TTCT | 2.06% |

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