Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:48:12 GMT 2023 |
| BAM file: | SRX7354181.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): | 50,691,717 / 50,649,246 |
| Number of aligned pairs (without duplicates): | 50,636,319 |
| Total number of alignments: | 109,071,547 |
| Number of secondary alignments: | 7,730,584 |
| Number of non-unique alignments: | 12,188,282 |
| Aligned to genes: | 86,655,448 |
| Ambiguous alignments: | 307,759 |
| No feature assigned: | 9,035,260 |
| Missing chromosome in annotation: | 884,798 |
| Not aligned: | 6,529,587 |
Reads genomic origin
| Exonic: | 86,655,448 / 90.56% |
| Intronic: | 5,169,163 / 5.4% |
| Intergenic: | 3,866,097 / 4.04% |
| Intronic/intergenic overlapping exon: | 3,564,266 / 3.72% |
Transcript coverage profile
| 5' bias: | 0.25 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 24,993,748 |
| ACCT | 5.28% |
| AGGT | 4.7% |
| ATCT | 4.14% |
| TCCT | 4.07% |
| AGGA | 3.29% |
| GCCT | 3.17% |
| CCCT | 2.83% |
| AGCT | 2.4% |
| AGGC | 2.23% |
| TTCT | 2.22% |
| AGAA | 1.98% |
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