Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:05:41 GMT 2023 |
| BAM file: | SRX7354230.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): | 44,796,353 / 44,753,547 |
| Number of aligned pairs (without duplicates): | 44,746,807 |
| Total number of alignments: | 94,583,027 |
| Number of secondary alignments: | 5,033,127 |
| Number of non-unique alignments: | 8,563,093 |
| Aligned to genes: | 76,301,632 |
| Ambiguous alignments: | 261,557 |
| No feature assigned: | 9,217,344 |
| Missing chromosome in annotation: | 239,401 |
| Not aligned: | 9,582,926 |
Reads genomic origin
| Exonic: | 76,301,632 / 89.22% |
| Intronic: | 6,084,217 / 7.11% |
| Intergenic: | 3,133,127 / 3.66% |
| Intronic/intergenic overlapping exon: | 3,071,367 / 3.59% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.77 |
Junction analysis
| Reads at junctions: | 27,960,186 |
| ACCT | 5.51% |
| AGGT | 4.81% |
| ATCT | 3.59% |
| AGGA | 3.42% |
| TCCT | 3.38% |
| GCCT | 3.14% |
| AGCT | 2.71% |
| AGGC | 2.47% |
| CCCT | 2.43% |
| AGAT | 2.16% |
| TTCT | 2.09% |
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