Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:00:07 GMT 2023 |
| BAM file: | SRX7354238.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): | 27,802,942 / 27,787,881 |
| Number of aligned pairs (without duplicates): | 27,785,923 |
| Total number of alignments: | 59,008,272 |
| Number of secondary alignments: | 3,417,449 |
| Number of non-unique alignments: | 5,663,668 |
| Aligned to genes: | 47,674,732 |
| Ambiguous alignments: | 168,739 |
| No feature assigned: | 5,248,034 |
| Missing chromosome in annotation: | 253,099 |
| Not aligned: | 3,010,313 |
Reads genomic origin
| Exonic: | 47,674,732 / 90.08% |
| Intronic: | 3,351,826 / 6.33% |
| Intergenic: | 1,896,208 / 3.58% |
| Intronic/intergenic overlapping exon: | 1,579,212 / 2.98% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.01 |
Junction analysis
| Reads at junctions: | 15,769,843 |
| ACCT | 5.54% |
| AGGT | 4.59% |
| ATCT | 3.58% |
| AGGA | 3.49% |
| GCCT | 3.43% |
| TCCT | 3.42% |
| AGCT | 2.67% |
| AGGC | 2.32% |
| CCCT | 2.28% |
| AGAT | 2.21% |
| TTCT | 2.2% |
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