Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:12:27 GMT 2023 |
| BAM file: | SRX7354334.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): | 34,181,836 / 34,128,589 |
| Number of aligned pairs (without duplicates): | 34,122,885 |
| Total number of alignments: | 82,606,174 |
| Number of secondary alignments: | 14,295,749 |
| Number of non-unique alignments: | 13,212,734 |
| Aligned to genes: | 52,160,391 |
| Ambiguous alignments: | 226,639 |
| No feature assigned: | 11,033,299 |
| Missing chromosome in annotation: | 5,973,111 |
| Not aligned: | 8,477,015 |
Reads genomic origin
| Exonic: | 52,160,391 / 82.54% |
| Intronic: | 6,898,587 / 10.92% |
| Intergenic: | 4,134,712 / 6.54% |
| Intronic/intergenic overlapping exon: | 2,401,829 / 3.8% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.35 |
| 5'-3' bias: | 1.66 |
Junction analysis
| Reads at junctions: | 20,706,194 |
| ACCT | 5.41% |
| AGGT | 4.55% |
| TCCT | 3.84% |
| ATCT | 3.52% |
| GCCT | 3.44% |
| AGGA | 3.17% |
| CCCT | 2.82% |
| AGCT | 2.52% |
| AGGC | 2.42% |
| TTCT | 2.15% |
| AGAT | 2% |

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