Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:31:03 GMT 2023 |
| BAM file: | SRX7354285.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): | 42,783,518 / 42,761,557 |
| Number of aligned pairs (without duplicates): | 42,755,426 |
| Total number of alignments: | 92,605,346 |
| Number of secondary alignments: | 7,060,271 |
| Number of non-unique alignments: | 10,411,634 |
| Aligned to genes: | 73,515,350 |
| Ambiguous alignments: | 346,357 |
| No feature assigned: | 7,165,298 |
| Missing chromosome in annotation: | 1,166,707 |
| Not aligned: | 2,328,623 |
Reads genomic origin
| Exonic: | 73,515,350 / 91.12% |
| Intronic: | 3,750,561 / 4.65% |
| Intergenic: | 3,414,737 / 4.23% |
| Intronic/intergenic overlapping exon: | 3,354,341 / 4.16% |
Transcript coverage profile
| 5' bias: | 0.14 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 23,119,113 |
| TCCT | 4.94% |
| ACCT | 4.76% |
| AGGT | 4.51% |
| ATCT | 4.39% |
| CCCT | 3.72% |
| AGGA | 3.1% |
| AGGC | 2.33% |
| GCCT | 2.33% |
| AGCT | 2.15% |
| TTCT | 2.07% |
| GTCT | 1.97% |
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