Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:49:52 GMT 2023 |
| BAM file: | SRX7354366.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): | 43,915,520 / 43,885,363 |
| Number of aligned pairs (without duplicates): | 43,877,800 |
| Total number of alignments: | 94,676,713 |
| Number of secondary alignments: | 6,875,830 |
| Number of non-unique alignments: | 11,024,144 |
| Aligned to genes: | 75,194,631 |
| Ambiguous alignments: | 324,076 |
| No feature assigned: | 7,471,814 |
| Missing chromosome in annotation: | 662,048 |
| Not aligned: | 2,364,129 |
Reads genomic origin
| Exonic: | 75,194,631 / 90.96% |
| Intronic: | 4,572,447 / 5.53% |
| Intergenic: | 2,899,367 / 3.51% |
| Intronic/intergenic overlapping exon: | 3,373,207 / 4.08% |
Transcript coverage profile
| 5' bias: | 0.21 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 2.01 |
Junction analysis
| Reads at junctions: | 27,026,674 |
| ACCT | 5.26% |
| ATCT | 4.95% |
| TCCT | 4.82% |
| AGGT | 4.15% |
| GCCT | 3.37% |
| CCCT | 3.09% |
| AGGA | 2.93% |
| TTCT | 2.28% |
| AGCT | 2.21% |
| AGGC | 2.06% |
| TCCC | 2.05% |
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