Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:50:50 GMT 2023 |
| BAM file: | SRX7354224.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): | 47,798,095 / 47,763,019 |
| Number of aligned pairs (without duplicates): | 47,740,269 |
| Total number of alignments: | 102,482,624 |
| Number of secondary alignments: | 6,921,510 |
| Number of non-unique alignments: | 11,496,742 |
| Aligned to genes: | 79,276,531 |
| Ambiguous alignments: | 295,038 |
| No feature assigned: | 10,879,073 |
| Missing chromosome in annotation: | 535,240 |
| Not aligned: | 1,311,686 |
Reads genomic origin
| Exonic: | 79,276,531 / 87.93% |
| Intronic: | 8,138,793 / 9.03% |
| Intergenic: | 2,740,280 / 3.04% |
| Intronic/intergenic overlapping exon: | 3,862,876 / 4.28% |
Transcript coverage profile
| 5' bias: | 0.53 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.1 |
Junction analysis
| Reads at junctions: | 31,681,594 |
| ACCT | 5.15% |
| AGGT | 4.85% |
| AGGA | 3.57% |
| ATCT | 3.35% |
| TCCT | 3.27% |
| AGCT | 2.87% |
| GCCT | 2.82% |
| AGGC | 2.47% |
| CCCT | 2.44% |
| AGAT | 2.2% |
| TTCT | 2.13% |
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