Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:27:10 GMT 2023 |
| BAM file: | SRX7354176.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): | 54,054,724 / 54,021,877 |
| Number of aligned pairs (without duplicates): | 54,017,634 |
| Total number of alignments: | 115,095,605 |
| Number of secondary alignments: | 7,019,004 |
| Number of non-unique alignments: | 11,428,245 |
| Aligned to genes: | 89,095,457 |
| Ambiguous alignments: | 272,508 |
| No feature assigned: | 13,685,732 |
| Missing chromosome in annotation: | 613,663 |
| Not aligned: | 3,817,363 |
Reads genomic origin
| Exonic: | 89,095,457 / 86.68% |
| Intronic: | 8,506,016 / 8.28% |
| Intergenic: | 5,179,716 / 5.04% |
| Intronic/intergenic overlapping exon: | 3,673,528 / 3.57% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 26,635,579 |
| ACCT | 5.43% |
| AGGT | 4.74% |
| AGGA | 3.62% |
| ATCT | 3.59% |
| TCCT | 3.46% |
| GCCT | 3.31% |
| AGCT | 2.62% |
| AGGC | 2.41% |
| CCCT | 2.39% |
| AGAT | 2.25% |
| TTCT | 2.21% |
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