Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:55:03 GMT 2023 |
| BAM file: | SRX7354226.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): | 37,885,526 / 37,868,493 |
| Number of aligned pairs (without duplicates): | 37,863,836 |
| Total number of alignments: | 80,774,520 |
| Number of secondary alignments: | 5,020,501 |
| Number of non-unique alignments: | 8,222,554 |
| Aligned to genes: | 65,483,693 |
| Ambiguous alignments: | 172,093 |
| No feature assigned: | 6,522,625 |
| Missing chromosome in annotation: | 373,555 |
| Not aligned: | 2,432,783 |
Reads genomic origin
| Exonic: | 65,483,693 / 90.94% |
| Intronic: | 4,039,644 / 5.61% |
| Intergenic: | 2,482,981 / 3.45% |
| Intronic/intergenic overlapping exon: | 2,229,404 / 3.1% |
Transcript coverage profile
| 5' bias: | 0.53 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 21,681,461 |
| ACCT | 5.09% |
| AGGT | 4.94% |
| ATCT | 3.95% |
| AGGA | 3.78% |
| TCCT | 3.78% |
| AGCT | 3.02% |
| GCCT | 2.7% |
| AGGC | 2.36% |
| AGAT | 2.21% |
| CCCT | 2.18% |
| TTCT | 2.11% |
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