Input data and parameters
Input
| Analysis date: | Tue Oct 31 14:14:08 GMT 2023 |
| BAM file: | SRX7354370.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): | 36,010,493 / 35,966,609 |
| Number of aligned pairs (without duplicates): | 35,945,505 |
| Total number of alignments: | 77,885,943 |
| Number of secondary alignments: | 5,908,841 |
| Number of non-unique alignments: | 9,901,506 |
| Aligned to genes: | 60,770,952 |
| Ambiguous alignments: | 260,415 |
| No feature assigned: | 6,553,372 |
| Missing chromosome in annotation: | 399,698 |
| Not aligned: | 3,460,168 |
Reads genomic origin
| Exonic: | 60,770,952 / 90.27% |
| Intronic: | 3,803,671 / 5.65% |
| Intergenic: | 2,749,701 / 4.08% |
| Intronic/intergenic overlapping exon: | 2,956,712 / 4.39% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 2.18 |
Junction analysis
| Reads at junctions: | 20,368,782 |
| ACCT | 5.5% |
| TCCT | 4.9% |
| ATCT | 4.58% |
| AGGT | 4.16% |
| CCCT | 3.33% |
| GCCT | 3.32% |
| AGGA | 2.84% |
| TTCT | 2.33% |
| AGCT | 2.2% |
| AGGC | 2.18% |
| TCCC | 2.03% |
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