Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:30:08 GMT 2023 |
| BAM file: | SRX7354249.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): | 31,585,753 / 31,558,365 |
| Number of aligned pairs (without duplicates): | 31,547,007 |
| Total number of alignments: | 68,219,661 |
| Number of secondary alignments: | 5,075,543 |
| Number of non-unique alignments: | 7,991,039 |
| Aligned to genes: | 52,906,605 |
| Ambiguous alignments: | 242,653 |
| No feature assigned: | 6,524,392 |
| Missing chromosome in annotation: | 554,972 |
| Not aligned: | 1,485,008 |
Reads genomic origin
| Exonic: | 52,906,605 / 89.02% |
| Intronic: | 4,419,013 / 7.44% |
| Intergenic: | 2,105,379 / 3.54% |
| Intronic/intergenic overlapping exon: | 2,993,674 / 5.04% |
Transcript coverage profile
| 5' bias: | 0.23 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.85 |
Junction analysis
| Reads at junctions: | 19,088,914 |
| ACCT | 4.99% |
| AGGT | 4.7% |
| ATCT | 4.08% |
| TCCT | 4.01% |
| AGGA | 3.19% |
| CCCT | 3.03% |
| GCCT | 2.86% |
| AGGC | 2.48% |
| AGCT | 2.41% |
| TTCT | 2.1% |
| AGAA | 1.88% |

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