Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:14:58 GMT 2023 |
| BAM file: | SRX7354282.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): | 39,897,390 / 39,879,538 |
| Number of aligned pairs (without duplicates): | 39,876,251 |
| Total number of alignments: | 83,836,422 |
| Number of secondary alignments: | 4,059,494 |
| Number of non-unique alignments: | 7,027,679 |
| Aligned to genes: | 69,640,242 |
| Ambiguous alignments: | 200,633 |
| No feature assigned: | 6,774,157 |
| Missing chromosome in annotation: | 193,711 |
| Not aligned: | 2,390,252 |
Reads genomic origin
| Exonic: | 69,640,242 / 91.13% |
| Intronic: | 3,466,300 / 4.54% |
| Intergenic: | 3,307,857 / 4.33% |
| Intronic/intergenic overlapping exon: | 2,444,468 / 3.2% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 2.19 |
Junction analysis
| Reads at junctions: | 22,535,627 |
| ACCT | 5.53% |
| AGGT | 4.97% |
| AGGA | 3.72% |
| ATCT | 3.59% |
| TCCT | 3.34% |
| GCCT | 2.93% |
| AGCT | 2.76% |
| AGAT | 2.43% |
| AGGC | 2.41% |
| CCCT | 2.29% |
| TTCT | 2.15% |
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