Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:32:26 GMT 2023 |
| BAM file: | SRX7354264.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): | 30,295,332 / 30,277,361 |
| Number of aligned pairs (without duplicates): | 30,273,897 |
| Total number of alignments: | 64,293,821 |
| Number of secondary alignments: | 3,721,128 |
| Number of non-unique alignments: | 5,676,950 |
| Aligned to genes: | 48,761,861 |
| Ambiguous alignments: | 178,229 |
| No feature assigned: | 9,174,220 |
| Missing chromosome in annotation: | 502,561 |
| Not aligned: | 1,267,935 |
Reads genomic origin
| Exonic: | 48,761,861 / 84.16% |
| Intronic: | 6,293,625 / 10.86% |
| Intergenic: | 2,880,595 / 4.97% |
| Intronic/intergenic overlapping exon: | 2,238,650 / 3.86% |
Transcript coverage profile
| 5' bias: | 0.52 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 18,223,811 |
| ACCT | 5.21% |
| AGGT | 4.73% |
| TCCT | 3.58% |
| ATCT | 3.57% |
| AGGA | 3.39% |
| GCCT | 3.33% |
| AGCT | 2.68% |
| CCCT | 2.68% |
| AGGC | 2.5% |
| TTCT | 2.25% |
| AGAT | 2.16% |

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