Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:28:23 GMT 2023 |
| BAM file: | SRX7354272.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): | 47,844,298 / 47,826,216 |
| Number of aligned pairs (without duplicates): | 47,822,259 |
| Total number of alignments: | 101,729,709 |
| Number of secondary alignments: | 6,059,195 |
| Number of non-unique alignments: | 9,828,113 |
| Aligned to genes: | 76,237,853 |
| Ambiguous alignments: | 264,309 |
| No feature assigned: | 14,806,915 |
| Missing chromosome in annotation: | 592,519 |
| Not aligned: | 2,363,440 |
Reads genomic origin
| Exonic: | 76,237,853 / 83.74% |
| Intronic: | 7,987,118 / 8.77% |
| Intergenic: | 6,819,797 / 7.49% |
| Intronic/intergenic overlapping exon: | 3,175,289 / 3.49% |
Transcript coverage profile
| 5' bias: | 0.45 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 1.89 |
Junction analysis
| Reads at junctions: | 25,716,422 |
| ACCT | 5% |
| AGGT | 4.72% |
| ATCT | 3.67% |
| TCCT | 3.53% |
| AGGA | 3.41% |
| GCCT | 3.23% |
| AGCT | 2.71% |
| CCCT | 2.7% |
| AGGC | 2.43% |
| TTCT | 2.28% |
| AGAT | 2.09% |
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